Inspection of the amino acid sequence of the bovine papillomavirus type 1 (BPV-1) E1 replication initiator/helicase protein revealed a single occurrence of a double histidine (HLH) motif characteristic of the signature HUH motif II of rolling-circle replication (RCR) initiator (Rep) proteins. Protein BLAST comparison of a portion of the BPV-1 E1 protein sequence containing this motif (a segment of the E1 protein bordering the N-terminal end of its minimal DNA binding domain (DBD)) with the Rep DBD of the parvovirus adeno-associated virus type 5 (AAV-5) produced an alignment of the AAV-5 Rep HLH motif with an HLQ motif in BPV-1 E1 which overlapped the E1 HLH motif in the pentameric sequence HLHLQ. Although the human papillomavirus type 16 (HPV-16) E1 protein did not contain the signature double histidine motif, CLUSTAL omega alignment of the full-length HPV-16 E1 and AAV-5 Rep proteins nevertheless revealed a precise correspondence of the AAV-5 Rep HLH motif II with an HIQ motif embedded centrally within the HPV-16 E1 DBD and also revealed a high degree of sequence similarity (homology) between sequences immediately C-terminal to the respective viral HLH/HIQ motifs. The BPV-1 and HPV-16 E1 sequences thus revealed, although from non-overlapping segments of the E1 protein, also exhibited substantial sequence similarity, suggesting that duplication of this part of the E1 gene had occurred, although at an early stage in the evolution of the E1 gene, before these papillomaviruses had diverged. In both BPV-1 and HPV-16, a threonine-containing RCR initiator motif I-like sequence (VLTP or GLTP) was found just proximal to the identified motif II-like sequences of each E1 protein. In the case of HPV-16, akin to the arrangement of RCR initiator motifs in the AAV-5 Rep protein, a tyrosine containing motif III-like sequence YWYK was present within a segment of the E1 DBD previously shown by X-ray crystallographic analysis of papillomavirus E1 proteins to form the alpha-5 helix of the DBD, which corresponds to the position of the reactive tyrosine-containing motif III of typical RCR initiator proteins. By contrast, the position of a potential motif III element(s) in the BPV-1 E1 protein sequence suggested a more complex regulation of expression of the predicted endonuclease function, for example by alternative splicing. We propose that E1 proteins with RCR initiator activity are expressed by BPV-1 and HPV-16 in growth-arrested or terminally differentiating cells, but that this function is suppressed during the maintenance or latent phase of the viral life cycle in proliferating virus transformed cells. On the basis of further original observations, we also propose that there is a mechanistic link between the processes of RCR and recombination-dependent replication (RDR).
©Stan Burnett