The push-and-pull evolution of tandem-duplicated drug-resistance genes
Two highly similar genes that contribute to drug resistance in a pathogenic yeast have been co-evolving as tandem duplicates for the past 134 million years—while maintaining distinct functions. This is the conclusion of a paper in the April issue of GENETICS by Lamping et al. that examines the evolutionary effects of ectopic gene conversion.
Evolutionary change can take a big step forward when a gene is duplicated within a genome. Gene duplication allows the new gene copy to diverge in function from the original, enabling new adaptations and innovations while preserving the ancestral activity. But duplicates can also be prevented from evolving differences because their sequence similarity encourages ectopic gene conversion, which transforms stretches of very similar sequence into identical matches. Normally, gene conversion corrects mismatched alleles that pair during meiosis; the process replaces the sequence from one allele with the corresponding part of the other allele, making the short paired region identical. Ectopic gene conversion (ECG) occurs between duplicated genes at separate loci that can undergo a similar gene conversion because of their high sequence similarity.
The similarity of tandem duplicates can make sequence analysis of the individual genes tricky. The authors tackled this task by analyzing the evolutionary patterns of two drug efflux pumps in Candida krusei, a disease-causing fungus that is naturally resistant to common antifungal drugs. Some of this yeast’s innate resistance comes from the activity of these two proteins, which pump toxic drugs out of the cell. The pumps arose from a tandem duplication event and have slightly different functions: one is more efficient at pumping out small molecules while the other specializes in removing larger compounds. By splitting the responsibility for pumping large and small molecules between the two gene products, natural selection enabled more efficient pumping of individual compounds by specializing each gene for its particular function.
The authors identified EGC events and small regions with adaptive differences between the two efflux pump gene duplicates by examining the sequence polymorphism of 30 different alleles of the two genes from seven different strains of the diploid C. krusei. Overall, a very high frequency of EGC events between both duplicates was indicated by low polymorphism. They detected EGC events by identifying alleles with shared nucleotide changes at the two separate duplicate loci. This copy/pasting process between highly similar sequences is clearly an important contributor to the evolution of these genes, as over 90% of the two duplicates were identical.
This similarity makes it even more remarkable that six short sections of DNA never experienced EGC, but instead they maintained distinct sequences between the two duplicate efflux pump genes. These differences cause changes in the protein sequence of the efflux pumps, particularly in the region that spans the cell membrane. Natural selection seems to be protecting these key functional differences from EGC, allowing the two copies to evolve specialized abilities in pumping molecules in and out of the cell. Comparing the sequence data from C. krusei with other species showed that the efflux pumps have been evolving together through EGC for roughly 134 million years. Lamping et al.’s work shows that though this force strongly pushes tandem duplicates towards similarity, natural selection is perfectly capable of pulling them back apart to fill unique adaptive roles.
Lamping, E., Zhu, J. Y., Niimi, M., & Cannon, R. D. (2017). Role of ectopic gene conversion in the evolution of a Candida krusei pleiotropic drug resistance transporter family. GENETICS, 205(4), 1619-1639.