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Journal of Virology, March 2006, p. 2958-2967, Vol. 80, No. 6
0022-538X/06/$08.00+0     doi:10.1128/JVI.80.6.2958-2967.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Exploring the DNA Binding Interactions of the Kaposi's Sarcoma-Associated Herpesvirus Lytic Switch Protein by Selective Amplification of Bound Sequences In Vitro

G.W. Hooper Foundation and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94143-0552

Received 12 August 2005/ Accepted 28 December 2005

The lytic switch protein RTA of Kaposi's sarcoma-associated herpesvirus (KSHV) can be targeted to DNA by either direct sequence-specific recognition or via protein-protein interactions with host transcription factors. We have searched for sequences capable of direct RTA binding by screening synthetic oligonucleotide pools and KSHV genomic libraries for RTA-interacting elements, using repeated cycles of in vitro binding followed by amplification of the bound sequences. Multiple low-affinity sequences were recovered from the random pools, with generation of only a weak consensus sequence. The genomic library, by contrast, yielded many biologically relevant fragments, most of which could be shown to interact with RTA in vitro and some of which likely play important regulatory roles in vivo. Surprisingly, the most highly selected fragment came from the promoter of a late gene (gB) and contained at least two direct RTA binding sites, as well as one RBP-J binding site. This raises the possibility that some late KSHV genes may also be subject to direct RTA regulation, though indirect models are not excluded.

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