The HIV-1 integrase IN catalyzes a critical step in the infectious cycle of this retrovirus. The mechanism leading to the integration of the proviral DNA into the host genome can be divided into two separate reactions (1). HIV-1 IN catalyzes first a hydrolytic reaction of the proviral DNA substrate, termed "processing," and second a transesterification step termed "joining" or "strand transfer," which allows the insertion of the provirus into the nuclear genome. In the processing reaction where OH Ϫ is the nucleophilic agent, IN is able to endonucleolytically remove in vitro two nucleotides from an oligonucleotide (ODN) mimicking the retroviral LTR ends of HIV-1. In the joining or strand transfer reaction, by using the processed LTR as a nucleophile, IN catalyzes a transesterification hydrolytic reaction. The resulting double-stranded proviral DNA is part of a large nucleoprotein structure termed the PIC. This complex contains the information necessary for nuclear localization and the enzymatic machinery required to insert the proviral DNA into the host genome (for a review of the PIC, see reference 4). In addition to IN and the proviral DNA, the PIC has been reported to contain various viral and cellular proteins. However, a precise description of the viral and cellular partners involved in this complex is not yet well defined.Although recombinant IN purified from Saccharomyces cerevisiae or bacteria can perform all the in vitro reactions using synthetic substrates (9), there is much evidence that proteins present in cytoplasmic extracts from uninfected cells are also involved in the integration process. Two proteins, the barrierto-autointegration factor and HMG I(Y), have been identified as specific cofactors (8,17). In addition, Kalpana et al. (21), using the yeast two-hybrid system, reported the isolation of a host factor, the integrase-interacting protein 1 (Ini1), as a binding partner of HIV-1 IN. Ini1 displays a high degree of sequence similarity to the yeast protein SNF5, a factor involved in the transcriptional activation of a number of genes.We have previously shown that the expression of HIV-1 IN in yeast induces a lethal phenotype (5), while the expression of an inactive mutated IN does not. These results strongly suggest that the lethal phenotype could be due to cell death by DNA damage induced by the IN activity. Moreover, the inactivation of the SNF5 transcription factor gene abolished the lethal phenotype induced by the expression of HIV-1 IN in yeast, indicating that SNF5 is able to interact with . Therefore, the use of the yeast system should facilitate the identification of IN-interacting proteins, thus allowing further studies in a cellular context by exploring the effect of gene inactivation on the IN-induced lethal effect.To identify yeast cellular proteins in addition to SNF5, whose human counterparts might participate in retroviral DNA integration, we developed an in vitro system to detect the interactions between HIV-1 IN and S. cerevisiae proteins. Using IN-affinity chromatography, we i...