Retroviruses integrate a DNA copy of their genome into host DNA as an obligatory step in their replication cycle. Our work focuses on the molecular mechanism of integration, and in particular on the structure and function of HIV integrase. Integrase is the viral enzyme that carries out the key DNA cutting and joining steps in the integration reaction. In the first step, 3' end processing, integrase cleaves two nucleotides from each 3' end of the viral DNA. In the second step, DNA strand transfer, the processed viral DNA ends are inserted into a target DNA. Recent studies have focussed on the interaction of viral DNA with the active site and on the interaction with an inhibitor obtained through a collaboration with Shionogi & Co. Ltd. We are also studying the mechanism of action of a novel cellular factor (BAF) that is involved in blocking self-destructive autointegration of retroviral DNA. BAF is a non-specific DNA binding protein that has the unusual property of bridging together DNA molecules. This results in intermolecular aggregation at high DNA concentration or intramolecular compaction at low DNA concentration. Our current model is that BAF blocks autointegration by compacting the viral DNA, making it inaccessible as a target for integration. Immunofluorescence and biochemical fractionation experiments show that BAF is present in both the nuclear and cytoplasmic compartments. The viral DNA can therefore acquire BAF passively from the cytoplasm without the need for a specific recruitment mechanism. We are investigating the role of BAF for the host cell. BAF interacts with LAP2, a protein that in turn binds to the Lamin proteins inside the nuclear envelope. The binding of BAF to both DNA and LAP2 suggests that it may play a role in anchoring chromatin to the nuclear envelope.
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