Comparison of Vpu sequences from diverse geographical isolates of HIV type1 identifies the presence of highly variable domains, additional invariantamino acids, and a signature sequence motif common to subtype C isolates

We compared the Vpu sequences from 101 strains of HIV-1 isolated from diver se geographical regions and various subtypes in order to identify regions o f high variability, and those amino acid residues that were highly conserve d or invariant. In addition to the highly conserved casein kinase II (CKII) phosphorylation sites, our analysis identified additional invariant residu es in the transmembrane domain and in the first and second alpha-helical do mains. Our analysis revealed that all subtype C sequences had a conserved L RLL motif at the C terminus that was also found in A/C intersubtype recombi nants. While our analysis demonstrated the conservation of CKII domains in HIV-1 group M and O isolates, the number of potential CKII phosphorylation sites was variable in SIVcpz sequences. The results of this study will prov ide a basis for future mutagenesis studies to examine the role of certain a mino acid residues in the structure and function of Vpu.