SPT5 and its binding partner SPT4 regulate transcriptional elongation by RNA polymerase II. SPT4 and SPT5 are involved in both 5,6-dichloro-1--D-ribofuranosylbenzimidazole (DRB)-mediated transcriptional inhibition and the activation of transcriptional elongation by the human immunodeficiency virus type 1 (HIV-1) Tat protein. Recent data suggest that P-TEFb, which is composed of CDK9 and cyclin T1, is also critical in regulating transcriptional elongation by SPT4 and SPT5. In this study, we analyze the domains of SPT5 that regulate transcriptional elongation in the presence of either DRB or the HIV-1 Tat protein. We demonstrate that SPT5 domains that bind SPT4 and RNA polymerase II, in addition to a region in the C terminus of SPT5 that contains multiple heptad repeats and is designated CTR1, are critical for in vitro transcriptional repression by DRB and activation by the Tat protein. Furthermore, the SPT5 CTR1 domain is a substrate for P-TEFb phosphorylation. These results suggest that C-terminal repeats in SPT5, like those in the RNA polymerase II C-terminal domain, are sites for P-TEFb phosphorylation and function in modulating its transcriptional elongation properties.Regulation of transcriptional elongation is a critical process in the control of viral and cellular gene expression (reviewed in references 3 and 28). A number of cellular factors that regulate transcriptional elongation have been defined using both biochemical and genetic techniques. These factors include the general transcription factors TFIIF and TFIIS, as well as other factors including the elongin and ELL proteins (20,41,48).In addition, cellular kinases play an important role in the control of transcriptional elongation based on their ability to phosphorylate the RNA polymerase II C-terminal domain (CTD) (27). One of these kinases, CDK-activating kinase (CAK), is composed of the CDK7 kinase in addition to cyclin H and MAT1. CAK is contained in the multiprotein TFIIH complex and is involved in modulating promoter clearance of specific promoters (13,45,47). A second kinase complex, PTEFb, is composed of cyclin T1 and CDK9 and also phosphorylates the RNA polymerase II CTD and stimulates transcriptional elongation (18,32,33,36,64). The Tat protein, which is a potent stimulator of transcriptional elongation, interacts with P-TEFb to stimulate human immunodeficiency virus type 1 (HIV-1) gene expression (4, 7, 17-19, 25, 26, 30, 31, 55, 56, 62, 64).SPT4 and SPT5 are highly conserved proteins which are present in a variety of species from yeast to humans and are involved in the regulation of transcriptional elongation (23,53,58,60,61). Genetic assays in yeast demonstrate that SPT5 conditional mutants can be suppressed by mutations in the genes encoding two largest subunits of RNA polymerase II (23). Furthermore, SPT5 interacts directly with RNA polymerase II via a domain in SPT5 that has homology to the Escherichia coli transcription elongation factor NusG (23, 53, 61). The human homologues of the SPT4 and SPT5 proteins have also been character...