Genetic specificity of DNA synthesized in the absence of T4 bacteriophage gene 44 protein

Multiple origins of replication contribute to a discontinuous pattern of DNA synthesis across the T4 genome during infection

Chromosomes provide a template for a number of DNA transactions, including replication and transcription, but the dynamic interplay between these activities is poorly understood at the genomic level. The bacteriophage T4 has long served as a model for the study of DNA replication, transcription, and recombination, and should be an excellent model organism in which to integrate in vitro biochemistry into a chromosomal context. As a first step in characterizing the dynamics of chromosomal transactions during T4 infection, we have employed a unique set of macro array strategies to identify the origins of viral DNA synthesis and monitor the actual accumulation of nascent DNA across the genome in real time. We show that T4 DNA synthesis originates from at least five discrete loci within a single population of infected cells, near oriA, oriC, oriE, oriF, and oriG, the first direct evidence of multiple, active origins within a single population of infected cells. Although early T4 DNA replication is initiated at defined origins, continued synthesis requires viral recombination. The relationship between these two modes of replication during infection has not been well understood, but we observe that the switch between origin and recombination-mediated replication is dependent on the number of infecting viruses. Finally, we demonstrate that the nascent DNAs produced from origin loci are regulated spatially and temporally, leading to the accumulation of multiple, short DNAs near the origins, which are presumably used to prime subsequent recombination-mediated replication. These results provide the foundation for the future characterization of the molecular dynamics that contribute to T4 genome function and evolution and may provide insights into the replication of other multi origin chromosomes.

A defective phage system reveals bacteriophage T4 replication origins that coincide with recombination hot spots

Plasmid transduction mediated by bacteriophage T4 has been used to study putative T4 DNA replication origins cloned as inserts in the Escherichia coli plasmid pBR322. Two particular inserts from the T4 genome allow high-frequency plasmid transduction, suggesting that each insert might contain a T4 replication origin. T4 infection of these plasmid-containing cells produces large numbers of defective phage particles that contain long linear concatamers of the plasmid DNA. During a second cycle of infection, these defective phage genomes can be replicated better than normal phage chromosomes present in the same infected cell; consequently, the T4 DNA inserts must be functioning as replication origins. Both of these origins appear to utilize a previously unrecognized mode of T4 replication initiation. Moreover, each origin coincides with a major recombination hot spot in the phage genome, and therefore this mode of replication initiation seems to involve a local stimulation of homologous genetic recombination. From a purely practical standpoint, additional DNA fragments can be cloned in an origin-containing plasmid, allowing isolation of large amounts of any DNA sequence with the glucosylated hydroxymethylcytosine modifications of T4 DNA.