Purification of the large mobilization protein of plasmid RSF1010 and characterization of its site‐specific DNA‐cleaving/DNA‐joining activity

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Abstract
A site‐specific and strand‐specific nick, introduced into the RSF1010 plasmid origin of transfer (oriT), initiates unidirectional DNA transfer during bacterial conjugation. We have previously reproduced this nicking at the duplex oriT in vitro using purified preparations of the three known RSF1010‐mobilization proteins: MobA (78‐kDa form of RSF1010 primase), MobB and MobC [Scherzinger, E., Lurz, R., Otto, S. & Dobrinski, B. (1992) Nucleic Acids Res. 20, 41–48]. In this study we report the purification of MobA to apparent homogeneity and demonstrate that this 78‐kDa protein by itself is capable of creating the oriT‐specific nick if the DNA is present in the single‐stranded form. By studying the cleavage of sets of oligodeoxyribonucleotides varying successively by single nucleotides at the 5′ or 3′ end, the minimal substrate for cleavage has been defined. The results identify the MobA recognition sequence within the 11‐residue oligonucleotide AAGTGCGCCCT which is cleaved at the 3′ side of the G at position 7. During the cleavage reaction, MobA becomes covalently linked to the 5′‐phosphate end of each broken DNA molecule and retains its activity for the rejoining reaction. It can transfer the attached DNA to an incoming acceptor strand provided that the DNA molecule contains at its 3′ end at least the seven nucleotides upstream of the nick site. The covalent MobA‐DNA linkage has been determined by two‐dimensional thin‐layer electrophoresis to be a tyrosyl phosphate. Extensive digestion of the 32P‐labeled MobA‐oligonucleotide complex with lysine carboxypeptidase yielded a single DNA‐bound peptide which was purified and sequenced. The resulting peptide sequence consists of amino acid residues at positions 22–30 in the MobA sequence and identifies Tyr24 as the residue linked to DNA in the covalent complex.