Computer-assisted dissection of rolling circle DNA replication.

A comparative analysis of the proteins involved in initiation and termination of rolling circle replication (RCR) was performed using computer-assisted methods of data based screening, motif search and multiple amino acid sequence alignment. Two vast classes of such proteins were delineated, one of these being associated with RCR proper, and the other with mobilization (conjugal transfer) of plasmid DNA. The common denominator of the two classes was found to be a conserved amino acid motif that consists of the sequence HisUHisUUU (U--bulky hydrophobic residue; hereafter HUH motif). Based on analogies with metalloenzymes, it is hypothesized that the two conserved His residues this motif may be involved in metal ion coordination required for the activity of the RCR and mobilization proteins. The proteins of the replication (Rep) class contained two additional conserved motifs, with the motif around the Tyr residue(s) forming the covalent link with nicked DNA being located C-proximally of the HUH motif. This class further split into two large superfamilies and several smaller families, with the proteins belonging to a single but not to different (super)families demonstrating statistically significant similarity to each other. Superfamily I, prototyped by the gene A proteins of small isometric single-stranded (ss) DNA bacteriophages, included also Rep proteins of P2-related double-stranded (ds) DNA bacteriophages, the small phage-plasmid hybrid phasyl, and several cyanobacterial and archaebacterial plasmids. These proteins contained two invariant Tyr residues separated by three partially conserved amino acids, suggesting that they all may share the cleavage-ligation mechanism proposed for phi X174 A protein and involving alternate covalent binding of both tyrosines to DNA (Van Mansfeld, A.D., Van Teeffelen, H.A., Baas, P.D., Jansz, H.S., 1986. Nucl. Acids Res. 14, 4229-4238). Superfamily II included Rep proteins of a number of ssDNA plasmids replicating mainly in gram-positive bacteria that unexpectedly were shown to be related to the Rep proteins of plant geminiviruses. Conservation of the "HUH" motif and a motif around the putative DNA-linking Tyr residue was observed also in the Rep proteins of animal parvoviruses containing linear ssDNA with a terminal hairpin and replicating via the rolling hairpin mechanism. The class of plasmid mobilization (Mob) proteins was characterized by the opposite orientation of the conserved motifs, with the (putative) DNA-linking Tyr being located N-proximally of the "HUH" motif.(ABSTRACT TRUNCATED AT 400 WORDS)