Discontinuous replication of colicin E1 plasmid DNA in a cell extract containing thermolabile DNA ligase

Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication

DNA polymerase I (pol I) processes RNA primers during lagging-strand synthesis and fills small gaps during DNA repair reactions. However, it is unclear how pol I and pol III work together during replication and repair or how extensive pol I processing of Okazaki fragments is in vivo. Here, we address these questions by analyzing pol I mutations generated through error-prone replication of ColE1 plasmids. The data were obtained by direct sequencing, allowing an accurate determination of the mutation spectrum and distribution. Pol I’s mutational footprint suggests: (i) during leading-strand replication pol I is gradually replaced by pol III over at least 1.3 kb; (ii) pol I processing of Okazaki fragments is limited to ∼20 nt and (iii) the size of Okazaki fragments is short (∼250 nt). While based on ColE1 plasmid replication, our findings are likely relevant to other pol I replicative processes such as chromosomal replication and DNA repair, which differ from ColE1 replication mostly at the recruitment steps. This mutation footprinting approach should help establish the role of other prokaryotic or eukaryotic polymerases in vivo, and provides a tool to investigate how sequence topology, DNA damage, or interactions with protein partners may affect the function of individual DNA polymerases.

DNA ligases from thermophilic bacteria enhance PCR amplification of long DNA sequences

Bacterial NAD-dependent Taq and Tth DNA ligases are capable of significantly increasing the yield of long PCR products when the amplification is carried out using bacterial family A DNA polymerases, e.g. Taq or Tth DNA polymerases, or with enzymatic blends containing these polymerases. We also show that Taq and Tth DNA ligases improve the results of PCR in the absence of NAD and therefore in the absence of DNA ligase activity. These observations suggest that bacterial DNA ligases can interact with these DNA polymerases, presumably as accessory proteins, thereby enhancing the efficiency of DNA polymerization.

DNA-protein interactions during replication of genetic elements of bacteria

Specific interactions of DNA with proteins are required for both the replication of deoxyribonucleic acid proper and its regulation. Genetic elements of bacteria, their extrachromosomal elements in particular, represent a suitable model system for studies of these processes at the molecular level. In addition to replication enzymes (DNA polymerases), a series of other protein factors (e.g. topoisomerases, DNA unwinding enzymes, and DNA binding proteins) are involved in the replication of the chromosomal, phage and plasmid DNA. Specific interactions of proteins with DNA are particularly important in the regulation of initiation of DNA synthesis. Association of DNAs with the cell membrane also plays an important role in their replication in bacteria.

Escherichia coli factor Y sites of plasmid pBR322 can function as origins of DNA replication

The Escherichia coli replication factor Y, in conjunction with other genetically undefined E. coli replication factors and the gene products of the E. coli dnaB, dnaC, and dnaG loci, is involved in de novo primer formation on the phi X174 (+) single-strand circular DNA template [(+) ss(c)DNA]. The participation of factor Y in this series of reactions is correlated with its phi X174 (+) ss(c)-specific DNA-dependent ATPase activity. Recently two factor Y effector DNA segments of the plasmid pBR322 have been identified in close proximity to the plasmid origin of DNA replication. We report here that insertion of these factor Y sites into the filamentous phage f1R229 (+) ss(c)DNA confers upon it the ability to be converted to RF DNA in vitro through a rifampicin-resistant dnaB, dnaC, and dnaG gene product-dependent pathway. Our data suggest that factor Y effector sites can function as origins of DNA replication.

DNA replication intermediates synthesized by lysates of dnaB, dnaG and dnaB dnaG mutants in vitro

Isogenic dnaB, dnaG, and dnaB dnaG mutants were constructed and used as extracts in the cellophane-disc in vitro DNA replication system. The increased proportion of 5S DNA characteristics of the dnab extract and the lack of Okazaki piece synthesis characteristic of the dnaG extract were both apparent in analysis of the dnaB dnaG mutant extract reaction. A hypothetical scheme to explain these results and those of others is presented.

Identification of two Escherichia coli factor Y effector sites near the origins of replication of the plasmids (ColE1 and pBR322

The Escherichia coli replication factor Y has been characterized as a phi X174 (+) strand specific DNA-dependent phosphohydrolase. In conjunction with other E. coli replication proteins, factor Y is involved in the formation of heterogeneous primers that are elongated by the E. coli DNA polymerase III elongation machinery. We report here that the heat-denatured DNAs of plasmids pBR322 and ColE1 serve as effectors for the hydrolysis of ATP by factor Y. The DNA sequences of pBR322 responsible for factor Y effector activity have been localized. Two separate regions of the pBR322 chromosome support Y ATPase activity. These sequences are near the replication origin and are located on opposite DNA strands.

Host components required for the replication of the resistance plasmid R124 and a copy mutant derivative

The replication of R124, and a copy mutant derivative of it, was measured with respect to dependence on the host DnaA, DnaB, DnaC, DnaE, DnaG, and PolA gene products. Both plasmids replicated under conditions where the DnaA gene product was inactivated or where the polymerising activity of the PolA gene product was reduced. In contrast, neither plasmid replicated to any appreciable extent, if the DnaB, DnaC, DnaE or DnaG gene products were inactivated. R124 integratively suppressed the lesion of the dnaA mutant but the copy mutant derivative had only a very weak suppressing effect. Neither plasmid suppressed the lesions of any of the other dna mutants.

Replication of the colicin E1 plasmid in extracts of Escherichia coli: uncoupling of leading strand from lagging strand synthesis

The replication of the ColEl plasmid was studied in extracts from E. coli dnaG mutants. It was found that the synthesis of the complementary strands of ColEl DNA can be carried out in these extracts in two consecutive steps: (1) synthesis of the leading L strand independent of the dnaG function, and (2) synthesis of the lagging H strand depending upon addition of wild-type dnaG protein. In contrast to L strand synthesis, the latter reaction is insensitive to rifampicin and novobiocin. Both synthetic pathways are however blocked by antiserum directed against dnaB protein. This indicates an additional role of the dnaB protein in duplex DNA replication besides assisting the dnaG protein in the priming of lagging strand synthesis. The T7 gene-4 protein acting in conjunction with T7 DNA polymerase can substitute for both the function of the dnaB and dnaG protein. It is concluded that plasmid replication proceeds by a semi-discontinuous mechanism.