Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region

Abstract

Fitness epistasis, the interaction among alleles at different loci in their effects on fitness, has potentially important consequences for adaptive evolution. We investigated fitness epistasis among amino acids of a functionally important region of the human immunodeficiency virus type 1 (HIV-1) exterior envelope glycoprotein (gp120). Seven mutations putatively involved in the adaptation of the second conserved to third variable protein region (C2-V3) to the use of an alternative host-cell chemokine coreceptor (CXCR4) for cell entry were engineered singly and in combinations on the wild-type genetic background and their effects on viral infectivity were measured. Epistasis was found to be common and complex, involving not only pairwise interactions, but also higher-order interactions. Interactions could also be surprisingly strong, changing fitness by more than 9 orders of magnitude, which is explained by some single mutations being practically lethal. A consequence of the observed epistasis is that many of the minimum-length mutational trajectories between the wild type and the mutant with highest fitness on cells expressing the alternative coreceptor are selectively inaccessible. These results may help explain the difficulty of evolving viruses that use the alternative coreceptor in culture and the delayed evolution of this phenotype in natural infection. Knowledge of common, complex, and strong fitness interactions among amino acids is necessary for a full understanding of protein evolution.

Figure 1.—

The HIV-1 ADA C2 (partial) and V3 gp120 protein regions. Engineered mutations are numbered and shown below the sequence. Underlined residues are putative N-linked glycosylation motifs.

Figure 2.—

The relative fitness of each engineered envelope assayed on cells expressing CCR5 or CXCR4. Error bars indicate 1 standard deviation. An asterisk (*) indicates statistically significant overall epistasis (ɛ), and a plus sign (+) indicates significant net epistasis for higher-order interactions (ɛ′).

Figure 3.—

Frequency distributions of epistatic deviation for statistically significant interactions on cells expressing CCR5 or CXCR4. Values on the epistatic deviation axis are upper bounds of the intervals. (A) Overall epistatic deviation. (B) Higher-order net epistatic deviation.

Figure 4.—

The frequency distribution of the magnitude of significant overall epistasis, E, on cells expressing CCR5 or CXCR4. Values on the magnitude axis are upper bounds of the intervals and are in units of orders of magnitude.

Figure 5.—

Minimum-length mutational trajectories on CXCR4 cells. The shortest observable mutational trajectories linking the CCR5-adapted wild-type ADA allele (wt), and the CXCR4-adapted ADA-1 allele (1234567), to the allele with the highest fitness when infecting cells expressing CXCR4 (13457). Mutations are numbered as in Figure 1. Only those mutation combinations that were engineered are shown. Solid arrows indicate single mutations that increase fitness. Shaded arrows indicate single mutations that do not increase fitness.