Evidence for adaptive evolution at the divergence between lymphoid and brain HIV-1 nef genes

Abstract

Human immunodeficiency virus type 1 (HIV) infection of the central nervous system frequently causes HIV-associated neurocognitive disorders (HAND). The role of HIV Nef and other accessory proteins in HAND pathogenesis is unclear. To determine whether HIV nef undergoes adaptive selection in brain, we cloned 100 nef sequences (n = 30 brain and n = 70 lymphoid) from four patients with AIDS and HIV-associated dementia (HAD). Normalized nonsynonymous substitutions were more frequent at the divergence of lymphoid and brain sequences, indicating stronger adaptive selection in brain compared to lymphoid tissue. Brain-specific nonsynonymous substitutions were found within an NH(3)-terminal CTL epitope, the PACS1 binding motif, or positions predicted to be important for activation of the myeloid-restricted Src family tyrosine kinase Hck. These results suggest that adaptive selection of HIV nef in brain may reflect altered requirements for efficient replication in macrophages and brain-specific immune selection pressures.

FIG. 1.

Phylogenetic analysis of brain- and lymphoid-derived Nef sequences. The consensus neighbor joining tree based on 10,000 reconstructions was created using MEGA 4.0 software using the Maximum Composite Likelihood method. The input CLUSTAL W nucleotide alignment included sequences from all patients and tissues. The scale bar (lower right) represents the length of a branch where 2 nucleotide substitutions occurred out of 100 total nucleotides. Significant bootstrap values (>95) representing the frequency out of 100 trees in which the node occurs are shown at the indicated positions.

FIG. 2.

Alignment of predicted brain- and lymphoid-derived Nef amino acid sequences. Consensus nucleotide sequences were generated using Bioedit software from CLUSTAL W alignments of each patient-specific tissue set of sequences in which the representative base occurred in at least 60% of sequences in the set. Consensus nucleotide sequences associated with each patient-specific tissue were used to generate a predicted amino acid sequence. The resulting amino acid sequences were aligned with CLUSTAL W. Residues of interest are in bold. “T Cell Epitope” indicates residues within reported CTL or CD4⁺ T helper epitopes. “PACS1 Binding” indicates residues interacting with the PACS1 protein. “SFK Binding” indicates residues that may influence the association of Nef with Src family kinases.