Selection of plasmid molecules for conjugative transfer and replacement strand synthesis in the donor

Conjugative DNA metabolism in Gram-negative bacteria

Bacterial conjugation in Gram-negative bacteria is triggered by a signal that connects the relaxosome to the coupling protein (T4CP) and transferosome, a type IV secretion system. The relaxosome, a nucleoprotein complex formed at the origin of transfer (oriT), consists of a relaxase, directed to the nic site by auxiliary DNA-binding proteins. The nic site undergoes cleavage and religation during vegetative growth, but this is converted to a cleavage and unwinding reaction when a competent mating pair has formed. Here, we review the biochemistry of relaxosomes and ponder some of the remaining questions about the nature of the signal that begins the process.

Replication and conjugative mobilization of broad host-range IncQ plasmids

The IncQ plasmids have a broader host-range than any other known replicating element in bacteria. Studies on the replication and conjugative mobilization of these plasmids, which have mostly been focused on the nearly identical RSF1010 and R1162, are summarized with a view to understanding how this broad host-range is achieved. Several significant features of IncQ plasmids emerge from these studies: (1) initiation of replication, involving DnaA-independent activation of the origin and a dedicated primase, is strictly host-independent. (2) The plasmids can be conjugatively mobilized by a variety of different type IV transporters, including those engaged in the secretion of proteins involved in pathogenesis. (3) Stability is insured by a combination of high copy-number and modulated gene expression to reduce metabolic load.

Identification of the origin of transfer (oriT) and DNA relaxase required for conjugation of the integrative and conjugative element ICEBs1 of Bacillus subtilis

Integrative and conjugative elements (ICEs), also known as conjugative transposons, are mobile genetic elements that can transfer from one bacterial cell to another by conjugation. ICEBs1 is integrated into the trnS-leu2 gene of Bacillus subtilis and is regulated by the SOS response and the RapI-PhrI cell-cell peptide signaling system. When B. subtilis senses DNA damage or high concentrations of potential mating partners that lack the element, ICEBs1 excises from the chromosome and can transfer to recipients. Bacterial conjugation usually requires a DNA relaxase that nicks an origin of transfer (oriT) on the conjugative element and initiates the 5'-to-3' transfer of one strand of the element into recipient cells. The ICEBs1 ydcR (nicK) gene product is homologous to the pT181 family of plasmid DNA relaxases. We found that transfer of ICEBs1 requires nicK and identified a cis-acting oriT that is also required for transfer. Expression of nicK leads to nicking of ICEBs1 between a GC-rich inverted repeat in oriT, and NicK was the only ICEBs1 gene product needed for nicking. NicK likely mediates conjugation of ICEBs1 by nicking at oriT and facilitating the translocation of a single strand of ICEBs1 DNA through a transmembrane conjugation pore.

Elements in the co-evolution of relaxases and their origins of transfer

The central elements in the conjugative mobilization of most plasmids are the relaxase and its cognate origin of transfer (oriT). The relaxase of the plasmid R1162, together with its oriT, belong to a large and widely distributed family of related relaxase/oriT pairs. Several of the properties of these elements are considered for R1162 and for other members of this family with a view to understanding how systems for mobilization might have evolved.

Mechanisms of strand replacement synthesis for plasmid DNA transferred by conjugation

A single strand of plasmid DNA is transferred during conjugation. We examined the mechanism of complementary strand synthesis in recipient cells following conjugative mobilization of derivatives of the IncQ plasmid R1162. A system for electroporation of donor cells, followed by immediate mating, was used to eliminate plasmid-specific replicative functions. Under these conditions, Escherichia coli recipients provided a robust mechanism for initiation of complementary strand synthesis on transferred DNA. In contrast, plasmid functions were important for efficient strand replacement in recipient cells of Salmonella enterica serovar Typhimurium. The mobilizing vector for R1162 transfer, the IncP1 plasmid R751, encodes a DNA primase with low specificity for initiation. This protein increased the frequency of transfer of R751 into Salmonella, but despite its low specificity, it was inactive on the R1162 derivatives. The R751 primase was slightly inhibitory for the transfer of both R751 and R1162 into E. coli. The results show that there is a chromosomally encoded mechanism for complementary strand synthesis of incoming transferred DNA in E. coli, while plasmid-specific mechanisms for this synthesis are important in Salmonella.

Molecular handcuffing of the relaxosome at the origin of conjugative transfer of the plasmid R1162

The assembly of plasmid-encoded proteins at a unique site (oriT) on the plasmid R1162, to form a complex called the relaxosome, is required for conjugative transfer of the plasmid and for negative regulation of neighboring promoters. Two-dimensional chloroquine gel electrophoresis was used to show that oriTs are physically coupled at the relaxosome. This interaction requires all the relaxosome proteins, which are assembled into a structure resulting in a decrease in the average linking number of the plasmid DNA in the cell. Molecules with higher superhelical densities are preferentially selected for assembly of the relaxosome. Genetic data obtained earlier indicate that the molecular coupling reported here is a 'handcuffing' reaction that contributes to the regulation of adjacent plasmid promoters. However, although these promoters affect the expression of the genes for replication, plasmid copy-control is regulated independently. This is the first time 'handcuffing' has been observed at an oriT, and its possible significance for transfer is discussed.

Conjugative DNA synthesis: R1162 and the question of rolling-circle replication

Strand-replacement synthesis during conjugative mating has been characterized by introducing into donor cells R1162 plasmid DNA containing a base-pair mismatch. Conjugative synthesis in donors occurs in the absence of vegetative plasmid replication, but with a lag between rounds of transfer, and with most strands being initiated at the normal site within the replicative origin. These characteristics argue against the idea that multiple plasmid copies are generated for successive rounds of transfer by rolling-circle replication. However, the R1162 relaxase protein can process molecules containing multiple transfer origins in the manner expected for the conversion of single-strand multimers, generated by rolling-circle replication, to unit-length molecules. This capability appears to be the result of a secondary cleavage reaction carried out by the protein. The possibility is raised that the processing of molecules with more than one origin of transfer might be a repair mechanism directed against adventitious DNA synthesis during transfer.