Drurey, J. R. | bioRxiv Science

bioRxiv2026

Eukaryotic domestication of a bacterial immune protein following horizontal transfer

Many components of eukaryotic innate immunity originated from bacterial immune systems. However, it is unclear how eukaryotes acquire these genes and how the components are domesticated into eukaryotic physiology. Here, we discovered a recent instance of bacteria-eukaryote horizontal transfer and used it to characterize the genetic and biochemical changes that accompanied eukaryotic acquisition. We focus on Toll/interleukin-1 receptor (TIR) domains, which are widespread yet potentially costly immune modules associated with inflammation and/or cell death. By generating an atlas of TIR diversity across the tree of life, we phylogenetically categorized the domains and uncovered highly diverged, eukaryotic TIR families. This analysis revealed a horizontal transfer event that created the TirBCD protein family of Dictyostelium amoebae, which is closely related to the bacterial immune protein TIR-STING. While the TIR domain was transferred into amoebae, the genomic locus did not contain known regulatory domains nor other components of a bacterial operon. Nevertheless, TirC retained biochemical and physiological similarities to TIR-STING. TirC is a highly potent NADase, capable of oligomerizing into large complexes and depleting NAD+ even at very low protein concentrations. When expressed in heterologous systems, TirC was spontaneously active and highly toxic. In contrast, the natural amoeba host tolerated expression of full length TirC, showing that the cells can typically regulate its activity and avoid autoimmunity. However, a truncated form of TirC induced rapid rounding and cell lysis. These results suggest that amoebae have used TirC to retool a form of bacterial cell death for use in eukaryotic cells. Overall, this study uncovers recent eukaryotic TIR evolution that captures features of both bacterial and eukaryotic immunity. We also expect that the TIR domain atlas will be useful to researchers across model systems as they explore the vast diversity of TIR molecular and cellular functions.

microbiology↗

bioRxiv2025

Hypermutable hotspot enables the rapid evolution of self/non-self recognition genes in Dictyostelium

Cells require highly polymorphic receptors to perform accurate self/non-self recognition. In the amoeba Dicytostelium discoideum, polymorphic TgrB1 & TgrC1 proteins are used to bind sister cells and exclude cheaters, but it remains unknown how cells continually generate this extreme genetic diversity. Here, we created a collection of chromosome-length, whole genome sequences from 10 Dictyostelium discoideum isolates and sister species to understand the evolution of the large tgr gene family. Our dataset includes AX2-214, a widely used D. discoideum lab strain, as well as complete genomes for two Chlamydia-like endosymbionts harbored within amoebae. We find that tgrB1 and C1 lie in a hypermutational hotspot, with haplotypes that undergo repeated intralocus recombination, duplications, transpositions, and inversions. These structural dynamics are highly localized adjacent to tgrB and C, resulting in the gain and loss of dozens of genes. The tgrBC genes themselves frequently duplicate and recombine, leading to the rapid generation of unique tgrBC repertoires. In the broader tgr gene family, some genes (e.g. tgrN) are single copy and syntenic across all the genomes, whereas others (e.g. tgrA) prolifically duplicate at similar rates to Dictyostelium transposons. Thus, the tgr genes are among the most rapidly evolving families genome-wide. We propose that the intense diversification within the tgrBC locus can help explain how these genes acquire such extreme levels of polymorphism, with parallels to the MHC immune genes in mammals and other allorecognition systems. This collection of amoeba genomes is also an ideal dataset for comparative genomics and molecular evolution in Amoebozoa. SignificanceThe ability to distinguish self from non-self is an essential part of innate immunity and multicellularity. In the amoeba Dicytostelium discoideum, cells form transient multicellular structures via aggregation. In the process, they exclude distantly-related cheater strains via highly polymorphic cell surface proteins, TgrB1 and TgrC1. We used this system to ask: how do organisms continually generate new variation in recognition factors? After sequencing a collection of Dictyostelium spp. genomes, we found that the tgrB and tgrC genes lie in an extraordinarily variable locus- a region with such high rates of gene birth and death that genomic similarities are quickly lost, even between closely related isolates. Thus, amoeba cell recognition mirrors self/non-self evolutionary dynamics found across the Tree of Life.

evolutionary biology↗