Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein

Epistatic interactions between residues determine a protein’s adaptability and shape its evolutionary trajectory. When a protein experiences a changed environment, it is under strong selection to find a peak in the new fitness landscape. It has been shown that strong selection increases epistatic interactions as well as the ruggedness of the fitness landscape, but little is known about how the epistatic interactions change under selection in the long-term evolution of a protein. Here we analyze the evolution of epistasis in the protease of the human immunodeficiency virus type 1 (HIV-1) using protease sequences collected for almost a decade from both treated and untreated patients, to understand how epistasis changes and how those changes impact the long-term evolvability of a protein. We use an information-theoretic proxy for epistasis that quantifies the co-variation between sites, and show that positive information is a necessary (but not sufficient) condition that detects epistasis in most cases. We analyze the “fossils” of the evolutionary trajectories of the protein contained in the sequence data, and show that epistasis continues to enrich under strong selection, but not for proteins whose environment is unchanged. The increase in epistasis compensates for the information loss due to sequence variability brought about by treatment, and facilitates adaptation in the increasingly rugged fitness landscape of treatment. While epistasis is thought to enhance evolvability via valley-crossing early-on in adaptation, it can hinder adaptation later when the landscape has turned rugged. However, we find no evidence that the HIV-1 protease has reached its potential for evolution after 9 years of adapting to a drug environment that itself is constantly changing. We suggest that the mechanism of encoding new information into pairwise interactions is central to protein evolution not just in HIV-1 protease, but for any protein adapting to a changing environment.

Evolution is often viewed as a process that occurs “mutation by mutation”, suggesting that the effect of each mutation is independent of that of others. However, in reality the effect of a mutation often depends on the context of other mutations, a dependence known as “epistasis”. Even though epistasis can constrain protein evolution, it is actually very common. Such interactions are particularly pervasive in proteins that evolve resistance to a drug via mutations that create defects, and that must be repaired with compensatory mutations. We study how epistasis between protein residues evolves over time in a new and changing environment, and compare these findings to protein evolution in a constant environment. We analyze the sequences of the human immunodeficiency virus type 1 (HIV-1) protease enzyme collected over a period of 9 years from patients treated with anti-viral drugs (as well as from patients that went untreated), and find that epistasis between residues continues to increase as more potent anti-viral drugs enter the market, while epistasis is unchanging in the proteins exposed to a constant environment. Yet, the proteins adapting to the changing landscape do not appear to be constrained by the epistatic interactions and continue to manage to evade new drugs.

Compilation and prevalence of mutations associated with resistance to non-nucleoside reverse transcriptase inhibitors

Background

Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are an important component of antiretroviral therapy for HIV type-1 (HIV-1)-infected patients. Development of NNRTI resistance can lead to treatment failure and is conferred by the presence of specific resistance-associated mutations (RAMs) in the reverse transcriptase. In addition to the widely used list of NNRTI RAMs provided by the International AIDS Society-USA HIV-1 Drug Resistance Mutation Group, which were identified on the basis of clinical experience with the approved NNRTIs, a more comprehensive list of NNRTI RAMs is needed to guide the study of baseline and emerging resistance to new NNRTIs.

Methods

We conducted an extensive review of the existing literature on NNRTI resistance, together with several in vitro and in vivo studies on the mechanism of HIV-1 resistance to approved NNRTIs and to NNRTIs formerly or currently in clinical development.

Results

In total, 44 NNRTI RAMs were identified. These included V90I, A98G, L100I, K101E/P/Q, K103H/N/S/T, V106A/I/M, V108I, E138G/K/Q, V179D/E/F/G/I, Y181C/ I/V, Y188C/H/L, V189I, G190A/C/E/Q/S, H221Y, P225H, F227C/L, M230I/L, P236L, K238N/T and Y318F. These NNRTI RAMs were observed, either alone or in combination with others, ranging in frequency from 0.02% to 56.96% in a panel of 101,679 NNRTI-resistant isolates submitted to Virco BVBA (Mechelen, Belgium) for routine clinical resistance testing. Phenotypical data from site-directed mutants helped to establish the contribution of each mutation to NNRTI resistance.

Conclusions

The list of 44 NNRTI RAMs compiled in this study provides a comprehensive overview of mutations that play a role in HIV-1 NNRTI resistance and can be used to guide further in vitro and in vivo research on the mechanisms of HIV-1 NNRTI resistance.