When a single amino acid makes all the difference

From the Geballe Lab, Human Biology Division

“Here, you see, it takes all the running you can do to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that,” the Red Queen tells Alice in Lewis Carrol’s Through the Looking Glass. Borrowing from this idea, the Red Queen hypothesis suggests that for viruses and hosts to simultaneously persist, they must continuously change. Viruses undergo evolutionary pressures which include, but are not limited to, differential hosts, immune responses, and/or antiviral drugs. Viruses exert evolutionary pressure on humans by introducing immune evasion mechanisms, hence fueling an evolutionary arms race whose outcome is determined by the rate and likelihood of adaptation by the host and the virus. At the molecular level, our cells produce interferon-induced proteins (antiviral proteins) to defeat pathogens, which, in turn, evolve mutations to avoid detection. An example of such a protein is MxB (Myxovirus Resistance Protein B), which has been  shown to inhibit the replication of retroviruses and herpesviruses in human hosts. Previous studies have identified MxB residues that are rapidly evolving; however, these changing residues are not critical for HIV restriction, suggesting that additional pathogens, such as herpesviruses, could have driven MxB's rapid evolution.  Dr. Avraham Bayer, a postdoctoral fellow in Dr. Adam Geballe's lab in the Human Biology Division, sought to determine whether the evolution of MxB has affected its capacity to inhibit herpesviruses. Recently, their findings were published in the Journal of Virology.

"There are many examples of evolutionary arms races occurring between hosts and their respective viruses. Often, the virus has adapted to overcome the host immune defenses,” Dr. Bayer commented. “We found that the host, humans in this case, seems to be “winning” in that arms race against herpes simplex virus 1.” “When cells were treated with IFN, HSV-1 infection was reduced. However, when MxB was knocked out of these cells, IFN treatment had significantly less impact on HSV-1 infection,” Dr. Bayer added. 

The restriction of HSV-1 is species specific. Only human MxB restricts HSV-1 replication.
The restriction of HSV-1 is species specific. Only human MxB restricts HSV-1 replication. Image provided by Dr. Bayer

Since the arms race between MxB and pathogens has led to MxB undergoing diversifying selection during primate evolution, the team asked whether MxB orthologs from non-primates (chimpanzees, African green monkeys, and owl monkeys) can inhibit herpesvirus replication (HSV-1 and HCMV-human cytomegalovirus). All MxB orthologs are capable of inhibiting HCMV replication, but only human MxB can inhibit HSV-1 replication, suggesting that MxB restriction of HSV-1 is species-specific. Furthermore, the team found that chimpanzee (chimp) MxB is capable of inhibiting HSV-2, which evolved following the transfer of the chimp simplex virus from chimpanzees to humans. These results highlight the species-specific nature of human MxB in restricting HSV-1.

Since both human MxB and chimp MxB have 98% sequence identity, it raises the question as to which species-specific amino acids allow human MxB to restrict to only HSV-1. The key residue in MxB was identified as codon 83, which encodes methionine in humans and lysine in most non-human primates. To test whether methionine at residue 83 was sufficient for HSV-1 inhibition, the team swapped out these residues in each species — replacing the lysine for methionine in chimp MxB and vice versa for human MxB. Consistent with their hypothesis, the lysine to methionine swap was sufficient to enable chimp MxB to inhibit HSV-1 replication, while the methionine to lysine substitution in human MxB resulted in loss of the ability to limit HSV-1 replication. These results indicate that the methionine at position 83 is critical for the antiviral function of MxB. From an evolutionary perspective, this indicates that a mutation in the common ancestor of humans led to the acquisition of a methionine codon in place of the lysine codon and thus led to HSV-1 restriction.

Interestingly, Dr. Geballe’s team identified a naturally-occurring “polymorphism that eliminates the ability of MxB to inhibit herpes simplex virus 1 in cell culture.” Approximately 2.5% of humans possess a threonine in position 83 that cannot inhibit HSV-1 replication. “This polymorphism might identify people at increased risks for severe herpes simplex virus disease,” said Dr. Bayer. Going forward, the team is interested in understanding the “mechanism underlying the different HSV-1 restriction abilities of M83 vs K83 or T83 in human MxB” as well as testing “whether M83 is unique in its ability to confer HSV-1 restriction or if other amino acids substitutions also retain unti-HSV-1 activity.”

The spotlighted research was supported by grants from National Institutes of Health and the Howard Hughes Medical Institute.  

Fred Hutch/University of Washington/Seattle Children's Cancer Consortium members Dr. Adam Geballe and Dr. Harmit Malik contributed to this work.

Bayer A, Child SJ, Malik HS, Geballe AP. A single polymorphic residue in humans underlies species-specific restriction of HSV-1 by the antiviral protein MxB. J Virol. 2023 Oct 5;97(10):e0083023. doi: 10.1128/jvi.00830-23. Epub ahead of print. PMID: 37796130; PMCID: PMC10617587.