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Phylogenetic analysis of novel dolphin (Tursiops truncatus) papillomavirus sequences, TtPV1, -2, and -3, indicates that the early and late protein coding regions of their genomes differ in evolutionary history. Sliding window bootscan analysis showed a significant a change in phylogenetic clustering, in which the grouped sequences of TtPV1 and -3 move from a cluster with the Phocoena spinipinnis PsPV1 in the early region to a cluster with TtPV2 in the late region. This provides indications for a possible recombination event near the end of E2/beginning of L2. A second possible recombination site could be located near the end of L1, in the upstream regulatory region. Selection analysis by using maximum likelihood models of codon substitutions ruled out the possibility of intense selective pressure, acting asymmetrically on the viral genomes, as an alternative explanation for the observed difference in evolutionary history between the early and late genomic regions of these cetacean papillomaviruses.

A 16-kb BamHI fragment of the lactose plasmid pNZ63 from Leuconostoc lactis NZ6009 was cloned in Escherichia coli MC1061 by using pACYC184 and was found to express a functional j-galactosidase. Deletion and complementation analysis showed that the coding region for ,-galactosidase was located on a 5. Mutation and deletion analysis showed that lacL expression is essential for LacM production and that both the lacL and lacM genes are required for the production of a functional 1-galactosidase in E. coli. The deduced amino acid sequences of the LacL and LacM proteins showed considerable identity with the sequences of the N-and C-terminal parts, respectively, of ,-galactosidases from other lactic acid bacteria or E. coli. DNA and protein sequence alignments suggest that the L. lactis lacL and lacM genes have been generated by an internal deletion in an ancestral 13-galactosidase gene.Two systems for lactose transport and hydrolysis among bacteria are known. The first system has only been found in gram-positive bacteria and involves a phosphoenolpyruvatedependent phosphotransferase system, by which lactose is phosphorylated during transport and subsequently hydrolyzed by a phospho-,B-galactosidase (for reviews, see references 14 and 22). In the second, more widespread system, lactose is transported across the cellular membrane by a galactoside permease, and the unmodified internalized sugar is hydrolyzed by a 13-galactosidase. Most research has focused on the lactose permease (lacY) and ,-galactosidase (lacZ) genes from Escherichia coli (for reviews, see references 3, 24, and 25), and its lacZ gene has been developed into a useful tool in molecular genetics. Similar lac genes located on chromosomal or plasmid DNA have been found in other gram-negative bacteria (20), and in one instance a lac transposon (Tn951) has been reported (11).Recently, lac genes have been characterized in lactic acid bacteria that are used as starter cultures in dairy fermentations and therefore are highly specialized lactose utilizers. Genetic studies have shown that the lactose-specific phosphotransferase system enzymes are homologous and plasmid encoded in Lactococcus lactis (14)(15)(16)30) and Lactobacillus casei (1, 2, 38). In contrast, the homologous lac genes of Streptococcus thernophilus and Lactobacillus bulgaricus are chromosomally located and have been found to encode unique lactose permeases (28, 37) and ,B-galactosidases that show high similarity to those of gram-negative bacteria (42,43). A plasmid-encoded P-galactosidase in Lactobacillus casei ATCC 393 has been reported (10). In addition, we showed recently that Leuconostoc lactis NZ6009 also contains a lactose plasmid that codes for a P-galactosidase (13). gram-positive cocci that are used for industrial milk and wine fermentations. We recently started the genetic characterization of Leuconostoc spp. (13) and focused on the plasmidlocated lac genes in L. lactis NZ6009 (12). Here we describe the molecular characterization of a DNA fragment from the lactose plasmid pNZ63 that ...

The genome of a novel virus, tentatively named bandicoot papillomatosis carcinomatosis virus type 2 (BPCV2), obtained from multicentric papillomatous lesions from an adult male southern brown bandicoot (Isoodon obesulus) was sequenced in its entirety. BPCV2 had a circular double-stranded DNA genome consisting of 7277 bp and open reading frames encoding putative L1 and L2 structural proteins and putative large T antigen and small t antigen transforming proteins. These genomic features, intermediate between Papillomaviridae and Polyomaviridae are most similar to BPCV1, recently described from papillomas and carcinomas in the endangered western barred bandicoot (Perameles bougainville). This study also employed in situ hybridization to definitively demonstrate BPCV2 DNA within lesion biopsies. The discovery of BPCV2 provides evidence of virus-host co-speciation between BPCVs and marsupial bandicoots and has important implications for the phylogeny and taxonomy of circular double-stranded DNA viruses infecting vertebrates.

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The healthy skin of two female domestic pigs (Sus scrofa domestica) was sampled with cottontipped swabs. Total genomic DNA was extracted from the samples and subjected to PCR with degenerate papillomavirus (PV)-specific primers. Similarity searches performed with BLASTN showed that partial E1 and L1 sequences of two novel PVs were amplified. Subsequently, the complete genomes of these Sus scrofa papillomaviruses (SsPVs) were amplified by longtemplate PCR, cloned and sequenced using a transposon insertion method. They contained the typical PV open reading frames (ORFs) E1, E2, E4, E6, L1 and L2, but the E7 ORF was absent in both viruses. Pairwise nucleotide sequence alignment of the L1 ORFs of the SsPVs showed 98.5 % similarity, classifying these viruses as SsPV type 1 'variants' (SsPV-1a and -1b). Based on a concatenated alignment of the E1, E2, L1 and L2 ORFs of SsPV-1 variants a and b, and 81 other human and animal PV type species, a neighbour-joining phylogenetic tree was constructed. This phylogenetic analysis showed that the SsPV-1a and -1b variants did not cluster with the other PVs of artiodactyls (cloven-hoofed) host species, but clustered on the edge of the genus Alphapapillomavirus, very near to the root of this genus.

Viruses of the family Polyomaviridae infect a wide variety of avian and mammalian hosts with a broad spectrum of outcomes including asymptomatic infection, acute systemic disease, and tumor induction. In this study a novel polyomavirus, the African elephant polyomavirus 1 (AelPyV-1) found in a protruding hyperplastic fibrous lesion on the trunk of an African elephant (Loxodonta africana) was characterized. The AelPyV-1 genome is 5722 bp in size and is one of the largest polyomaviruses characterized to date. Analysis of the AelPyV-1 genome reveals five putative open-reading frames coding for the classic small and large T antigens in the early region, and the VP1, VP2 and VP3 capsid proteins in the late region. In the area preceding the VP2 start codon three putative open-reading frames, possibly coding for an agnoprotein, could be localized. A regulatory, non-coding region separates the 2 coding regions. Unique for polyomaviruses is the presence of a second 854 bp long non-coding region between the end of the early region and the end of the late region. Based on maximum likelihood phylogenetic analyses of the large T antigen of the AelPyV-1 and 61 other polyomavirus sequences, AelPyV-1 clusters within a heterogeneous group of polyomaviruses that have been isolated from bats, new world primates and rodents.

The first fully sequenced papillomavirus (PV) of marsupials, tentatively named Bettongia penicillata papillomavirus type 1 (BpPV1), was detected in papillomas from a woylie (Bettongia penicillata ogilbyi). The circular, double-stranded DNA genome contains 7,737 bp and encodes 7 open reading frames (ORFs), E6, E7, E1, E2, E4, L2, and L1, in typical PV conformation. BpPV1 is a close-to-root PV with L1 and L2 ORFs most similar to European hedgehog PV and bandicoot papillomatosis carcinomatosis virus types 1 and 2 (BPCV1 and -2). It appears that the BPCVs arose by recombination between an ancient PV and an ancient polyomavirus more than 10 million years ago.