Figure 2

Schematic of WT LAI and LAINef dd . Three bars represent nef coding sequence and the U3 sequence for LAI, LAINefdd and patient SG1 clone 27 sequence [35]. SG1 clone 27 reflects the tendency of patients with defective nefs to lose all remaining coding sequence [5, 7, 35, 36]. The coding sequence of WT type LAI nef (NCBI Accession, K02013) is presented in the top bar (nucleotides 8390–9010). PPT, polypurine tract is nucleotides 8662–8678. U3 consists of nucleotides 8678 to 9132. The core U3 promoter elements include two NF-κB binding sites, three SP1 sites and the TFIID binding site or TATA box. In the lower bar the 5’ deletion incorporated into LAINefdd is 114 nucleotides (8495–8608). Within the deletion, a four base insertion was added to create a frame shift (See Methods). The 3′ gap in LAINefdd is a frame-shifting deletion of 290 bases (8692–8981). In the middle bar the deletions in SG1 isolate 27 are aligned with LAI. The gaps are not numbered for simplicity of presentation. The 5′ deletion in SG1 is 217 nucleotides and the 3′ deletion is 292 nucleotides.