Human Genetics Graduate Student
I presented "Escape from bacterial iron piracy through rapid evolution of transferrin” (Barber and Elde, Science, 2014) at the human genetics journal club on 12/9/15.
Pathogen infections have been thought to represent a major selective pressure in primate evolution. Encounters of hosts and pathogens results in an evolutionary arms race, in which the host is under pressure to evolve pathogen resistance, and the pathogen is under pressure to counteract host resistance. This cyclical adaptation of both hosts and pathogens, referred to as the Red Queen scenario, results in a persistent evolutionary conflict, the genetic imprints of which may be found embedded in primate genomes. A key goal, therefore, is to identify the genetic determinants of repeated adaptations and counter-adaptations in host-pathogen genomes and understand its evolution. This paper highlights how evolutionary genetic approaches can be used to elucidate the genetic basis of host-pathogen interactions in nutritional immunity. Barber and Elde have used a cool integration of primate phylogenetics, population genetics, and molecular functional characterization to demonstrate such an evolutionary arms race, using an example centered on iron sequestration in great apes.
Using primate phylogenetics and structural biology, the authors have nicely shown that transferrin, the protein involved in vertebrate iron sequestration, is subject to rapid pathogen-driven evolution on the primate lineage. The rapidly evolving sites in transferrin map on to the interface of transferrin and transferrin binding protein A, a protein produced by bacterial pathogens such as Neisseria and Hemophilus to hijack host nutritional immunity. To examine the functional consequences of rapid evolution at this interface, the authors used competitive binding assays to demonstrate host specificity of pathogens on the primate phylogeny. Turns out that both human and gorilla transferrin are recognized by the two pathogens, but chimpanzees and other great apes have evolved adaptations in their transferrin proteins to evade bacterial iron piracy. To determine the genetic basis of pathogen adaptation, the authors used evolutionary genetics approaches to show that as little as a single amino acid substitution is sufficient to confer resistance on the chimpanzee lineage. However, this amino acid is not fixed in other great apes that are resistant to the tested pathogens, suggesting that other amino acid residues may be conferring adaptations in these lineages. Further, this work has answered a long-standing question that has been perplexing biochemists and evolutionary biologists for years: the cause of standing genetic variation at the transferrin locus in humans. Population genetic analyses combined with functional assays showed that while the major transferrin allele, C1, is susceptible to pathogen attack, the C2 allele confers strong to intermediate resistance against several pathogen strains. This explains why the C2 allele has persisted in many human populations.
One great strength of this paper lies in testing lineage-specific pathogen adaptations in a phylogenetic framework involving many great apes. This makes lineage specific losses and gains of adaptations clearly interpretable, with comprehensive functional testing beyond just a few species on the phylogeny. The population genetics analyses combined with functional work has been deeply insightful in illuminating the cause of standing genetic variation. Despite having employed strong evolutionary and structural biology approaches, there are some limitations on the functional side. One major shortcoming of this work is the assay chosen to quantify the interaction between primate transferrin, and bacterial transferrin binding protein A. The authors used dot blot competitive binding assays, which are rather difficult to interpret. The normalized A450 estimates, which quantify the strength of interaction between transferrin and transferrin binding protein A, are not at equilibrium, and certainly not equivalent to the Kd of binding. This makes it very difficult to evaluate the weak to intermediate affinities of binding between the two proteins (see figs. 2 and 3). This issue also becomes relevant while evaluating the functional importance of standing genetic variation in two human transferrin alleles, C1 and C2. The authors claim that the C1 allele is susceptible to attack by all pathogens, while the C2 allele confers strong to intermediate resistance against some tested pathogen strains (fig. 3). The authors have concluded potential evolutionary trade-offs between intermediate affinities of binding and broad host-range specificities based on these estimates. However, the employed assay does not calculate affinities, making any claims about evolutionary trade-offs uninterpretable. It is unclear why the authors refrained from using other biochemical assays, such as fluorescence polarization to quantify host-pathogen interactions. Further, the evolution of new pathogen strains in response to recently acquired host adaptations could have been better illuminated in the context of pathogen phylogenies. How do new pathogen strains emerge in the context of host adaptations is a central question in molecular evolution, and the data presented in this paper provide ample opportunities to address this.
Despite the above limitations, this paper has nicely demonstrated how an evolutionary arms race in the battle for iron played out over 40 million years, thereby drawing parallels between nutritional immunity and adaptive immunity for the first time. Other than the obvious clinical relevance of this work, the integrative approaches described here could be broadly applicable to other systems that involve piracy of host machinery, such as bacteria/bacteriophage interactions, gut microbiome/host proteins and plant/ plant pathogen infections.
Editor: Vincent Lynch, Assistant Professor, Dept of Human Genetics