To investigate the transcriptional mechanisms of rice tungro bacilliform virus, we have systematically analyzed an activator element located immediately upstream of the TATA box in the rice tungro bacilliform virus promoter and its cognate trans-acting factors. Using electrophoretic mobility shift assays, we showed that rice nuclear proteins bind to the activator element, forming multiple specific DNA-protein complexes via protein-protein interactions. Copper-phenanthroline footprinting and DNA methylation interference analysis indicated that multiple DNA-protein complexes share a common binding site located between positions ؊60 to ؊39, and the proteins contact the activator element in the major groove. DNA UV cross-linking assays further showed that two nuclear proteins (36 and 33 kDa), found in rice cell suspension and shoot nuclear extracts, and one (27 kDa), present in root nuclear extracts, bind to this activator element. In protoplasts derived from a rice (Oryza sativa) suspension culture, the activator element is a prerequisite for promoter activity and its function is critically dependent on its position relative to the TATA box. Thus, transcriptional activation may function via interactions with the basal transcriptional machinery, and we propose that this activation is mediated by protein-protein interactions in a position-dependent mechanism.In eukaryotes, the transcription of protein-coding genes by RNA polymerase II is regulated via two distinct types of DNA sequences: core promoter elements, located near the transcription start site that are sufficient to direct the accurate initiation of transcription; and upstream promoter elements, which contain binding sites for sequence-specific transcriptional activator and/or repressor proteins (1, 2). Transcriptional activators stimulate transcription by recruiting the RNA polymerase II machinery to a core promoter and/or stabilizing the transcription-initiation complex (3-6). Activators have been proposed to directly or indirectly (through coactivators) interact with components of the basal transcription machinery in mammalian systems (3,7,8).Although the basal transcriptional machinery, also referred to as the polymerase II transcription initiation complex, has not been studied in plants as extensively as in mammalian, Drosophila, and yeast systems, TATA-binding proteins (TBPs), 1 TFIID, TFIIA, and RNA polymerase II subunits have been isolated from plants (9 -12). Moreover, a number of plant trans-acting factors have been identified (13). Little is known in plants about the molecular mechanisms of transcriptional activation. It has been shown that TGA1a, a transcription activator interacting with the activation sequence-1 element in the CaMV 35 S promoter (14), increases the rate of preinitiation complex formation (15, 16). The plant transcription factor GT-1 belongs to the class of trihelix DNA-binding proteins, and it binds to a promoter cis-element with the core DNA sequence 5Ј-GGTTAA found initially in light-regulated genes (17). Recently, it has bee...