The κB DNA sequence from the HIV long terminal repeat functions as an allosteric regulator of HIV transcription

Abstract

NF-κB is an inducible transcription factor involved in the immune response, inflammation, and viral transcription. To address how the two NF-κB and three Sp1 binding sites of the human immunodeficiency virus (HIV) long terminal repeat (LTR) control multiple activator assembly and transcription, we first observed and compared unique conformations between the crystallographic structure of the NF-κB p50·p65 heterodimer bound to the uPA-′B target site to that of the p50·p65·HIV-κB complex. Next, cooperativity between two NF-κB molecules bound to tandem HIV-κB sequences was measured as well as that of NF-κB and transcription factor Sp1 when bound to adjacent sites. The cooperativity of hybrid HIV-LTR enhancers was measured with the 3′ κB site converted to uPA-κB or to interferon β gene enhancer κB. The hybrids were defective in transcriptional activator assembly and less active transcriptionally. These functional differences correlate with observed conformational differences and demonstrate that distinct κB DNA sequences function as allosteric regulators in a gene-specific manner.