We want to understand DNA replication and its relationship to recombination, transcription, repair and packaging of DNA, in the context of understanding physiological connections and transitions between basic processes acting on DNA during different developmental stages and during the parasitic relationship of viruses and their hosts in pathogenic situations. Like many other viruses, phage T4 uses several different modes to initiate DNA replication forks: primary origin initiation, recombination-dependent initiation and a less well- characterization tertiary mode. We want to study these specific processes and their physiological connections combining genetic and biochemical methods by analyzing interactions of individual genes, proteins and protein complexes with each other and with target DNA. Our efforts are concentrated towards the following specific problems: a) A comparison of primary origins of DNA replication, mainly oriA and oriF, where the latter also operates in the secondary and tertiary mode. b) The roles of in-frame overlapping proteins encoded in three regions--the oriA region, gene 49 (encoding a recombination endonuclease), and gene 17 (encoding a packaging protein). c) The roles of DNA topoisomerases in recombination, DNA replication and transcription. d) Interactions or interference of these proteins with other phage and host proteins that affect transcription, replication, recombination, and repairs. These specific questions are interrelated by increasing evidence that several of the proteins under study participate in several different albeit related protein machines, thereby participating in or competing with different processes. In-frame overlapping peptides encoded by the same gene may play a physiologically important role in macromolecular assemblies and in altering compositions of such complexes during transitions occurring in viral development. Sharing of proteins in different complexes superimposes an added dimension to individual controls of macromolecular processes which operate in virus-infected cells and during normal development. The well-development genetics and biochemistry of T4 makes this virus a prime object for analyzing such supramolecular controls.
