In a groundbreaking discovery that reshapes our understanding of bacterial immunity, recent research has unveiled a novel immune signaling molecule produced by Toll/interleukin-1 receptor (TIR) domains in bacteria. Historically recognized as essential components of innate immune systems across all domains of life, TIR domains have been primarily appreciated for their role in detecting pathogenic threats and triggering immune responses. Now, the identification of a unique conjugate molecule, histidine-ADP-ribose (His-ADPR), reveals an unprecedented mode of bacterial immune signaling that intricately links nucleotide and amino acid biochemistry.
TIR domains have long been established as pivotal pattern recognition modules in diverse organisms, ranging from bacteria to plants and animals. Their conserved presence underlines their evolutionary importance in sensing pathogen invasion and orchestrating defenses. In bacteria and plants, these domains exert their immunological function through the generation of small signaling molecules that are exclusively composed of nucleotide moieties. This nucleotide-centric signaling paradigm governed immune recognition and downstream activation until the present study revealed an unexpected biochemical twist.
The research focused on the type II Thoeris defense system in bacteria, a specialized immune mechanism that deploys TIR-domain proteins to detect viral (phage) infection. Through sophisticated enzymatic assays and structural biology, the team demonstrated that bacterial TIR domains generate a signaling molecule fundamentally different from previously known products. This molecule uniquely combines the nucleotide ADP-ribose with the amino acid histidine, thus termed histidine-ADP-ribose (His-ADPR). This discovery expands the molecular vocabulary of immune signals beyond nucleotide-only frameworks, showing an innovative fusion motif in bacterial immune chemistry.
Remarkably, His-ADPR is synthesized in the bacterial cytoplasm specifically in response to phage infection, signifying a targeted and infection-responsive immune signaling event. Upon production, His-ADPR serves as a potent activator of the Thoeris effector protein. The effector is equipped with a Macro domain located at its C-terminal end, which exhibits a high-affinity binding pocket tailored to recognize and bind His-ADPR. This molecular interaction triggers downstream antibacterial responses, effectively halting phage proliferation and preserving bacterial viability.
Key to understanding this interaction, the researchers solved the crystal structure of the ligand-bound Macro domain at atomic resolution. The structure revealed precise molecular contacts between the Macro domain and both components of His-ADPR: the adenine nucleobase, the ribose-phosphate backbone, and critically, the histidine moiety. This structural insight elucidates the specificity and mechanistic basis for His-ADPR recognition, explaining how the bacterial immune system selectively senses this hybrid molecule as an immune alarm.
Further biochemical and mutational analyses illuminated the functional consequences of this binding. Mutations in the Macro domain that disrupt His-ADPR engagement abolish immune activation, underscoring the indispensability of this binding event in bacterial antiviral defense. Conversely, mutations targeting the enzymatic TIR domain abrogate the synthesis of His-ADPR itself, thereby disabling the immune signaling cascade. Together, these findings firmly anchor His-ADPR as a critical immune mediator in the Thoeris defense pathway.
Intriguingly, the study revealed a clever evolutionary countermeasure employed by phages to evade this bacterial immune response. The researchers identified a family of phage-encoded proteins capable of binding and sequestering His-ADPR molecules, effectively neutralizing the immune signal. By scavenging His-ADPR, these viral proteins prevent effector activation, allowing phages to circumvent Thoeris-mediated immunity and successfully infect their bacterial hosts. This arms-race dynamic highlights the sophisticated molecular interplay between bacteria and their viral predators.
This novel class of TIR-derived immune signals that marry nucleotide and amino acid components challenges the prevailing dogma of nucleotide-only immune messengers and expands the biochemical diversity of immune signaling. The addition of an amino acid to the signaling molecule may confer unique chemical properties, stability, or receptor specificity, opening new avenues for exploring immune regulation mechanisms in prokaryotes. The discovery prompts a reevaluation of TIR domain enzymology and the range of possible immune signals generated by these versatile protein modules across life.
Moreover, the identification of His-ADPR as a bacterial immune signal parallels and contrasts the signaling strategies employed in plants and animals, where TIR domain functions and downstream effectors exhibit diverse biochemical adaptations. This finding offers exciting prospects for comparative immunology and evolutionary biology, providing a molecular snapshot of how immune signaling complexity has diversified in response to unique ecological pressures, such as viral predation.
From a practical standpoint, understanding the detailed mechanisms of His-ADPR signaling and evasion may open new prospects for antibacterial therapeutics and biotechnology. By targeting the synthesis or recognition of His-ADPR, it might be possible to modulate bacterial immunity or disrupt phage infections with precision. Additionally, phage-encoded His-ADPR-binding proteins could serve as molecular tools to manipulate ADP-ribosylation-related pathways or to engineer synthetic immune circuits.
The integration of structural biology, enzymology, and microbiology in this study showcases the power of multidisciplinary approaches to dissect immune signaling at the molecular level. As the team continues to explore the broader distribution and functional diversity of His-ADPR signaling across bacterial species, it is likely that further variations and adaptations of this immune motif will be uncovered, revealing a richer landscape of bacterial immune strategies than previously anticipated.
This research not only rewrites the biochemical lexicon of bacterial innate immunity but also underscores the vast, largely untapped molecular innovations harbored within microbial defense systems. Such discoveries promise to fuel future investigations at the interface of structural biology, immunology, and microbial ecology, ultimately shaping our capacity to harness and combat microbial life in diverse contexts.
Subject of Research: Bacterial TIR-domain proteins and immune signaling via histidine-ADP-ribose (His-ADPR) in response to phage infection.
Article Title: TIR domains produce histidine-ADPR as an immune signal in bacteria.
Article References:
Sabonis, D., Avraham, C., Chang, R.B. et al. TIR domains produce histidine-ADPR as an immune signal in bacteria. Nature (2025). https://doi.org/10.1038/s41586-025-08930-2
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