Mycobacterium tuberculosis infects one-third of the world's population and causes two million deaths annually. Its intracellular residence raises the possibility that bacterial nucleic acids might interact with key host proteins and contribute to the pathophysiology of infection. To test this hypothesis, we searched for motifs closely resembling eukaryotic transcription factor binding sites in the M. tuberculosis H37Rv genome and found activator protein-2 and zinc finger protein-5 binding motifs in a 36-nucleotide repetitive mycobacterial DNA sequence (RPT1). RPT1 bound specifically to nuclear extract proteins from U937, A549, and HeLa cells in electrophoretic mobility shift assays but not to activator protein-2. Several nuclear and cytosolic proteins showing at least partial binding specificity for RPT1 were isolated from U937 and A549 cells by pull-down assays, including Ku70 (DNA-dependent protein kinase subunit) and poly(ADP-ribose) polymerase-1. RPT1 also specifically activated DNA-dependent protein phosphorylation. These results suggest that mycobacterial nucleic acid fragments may interact specifically with eukaryotic regulatory proteins which might contribute to bacterial life-cycle maintenance. (C) 2004 Elsevier Inc. All rights reserved.