Why this glossary
Molecular biology has a technical vocabulary that scares off three out of four readers on the first page. It is a shame. Behind each word lies a story that would make it obvious. We will unfold the blocks of the anti-phage arsenal by telling their story each time.
Do not read everything at once. Come back and pick when you encounter an unknown word in a workshop or a chapter.
The actors
Phage
A virus that infects bacteria. Not humans. You have a few trillion on your skin and in your gut right now. They are totally indifferent to you. Fun fact: there are more of them than stars in the observable universe. They are also called bacteriophages (“bacteria eaters”). Félix d’Hérelle coined the term at the Institut Pasteur in 1917—long before we understood what they were.
Host bacterium
The attacked cell. When the phage injects its DNA into it, there are two outcomes. Either the bacterium lets itself be hijacked and produces 100 new phages before bursting (death by lysis, which is ugly). Or it triggers a defense system and dies before being hijacked—an altruistic suicide that saves its neighbors.
Defense system
An operon (= a cluster of contiguous genes regulated together) that detects a phage and triggers a response. 478,206 different families were cataloged in 2026 (Bernheim et al., Science). We thought there were six ten years ago. The bacterial world is much more bellicose than we thought.
The parts of a system
Sensor
The protein that detects the infection. Often an ATPase that spots foreign DNA, or a receptor that detects a characteristic phage signal. If you want an analogy: it is the fire alarm.
Effector
The protein that acts. It cleaves phage RNA, degrades an essential translation cofactor, or destroys the bacterial membrane. If the sensor is the alarm, the effector is the firefighter—and often, incidentally, the fire too (cell suicide).
Transducer / Auxiliary
Between sensor and effector, there is sometimes a third protein that amplifies the signal or translates it from one chemical nature to another. In CBASS, it is the cyclase that transforms a DNA detection into a soluble cGAMP signal.
Second messenger
A small molecule (often cyclic: cGAMP, cCMP, cUMP, c-di-AMP) produced by the sensor and recognized by the effector. It is a diffusible signal, like an internal cell hormone. Fun fact: the same chemical grammar exists in humans (cGAS-STING uses cGAMP). Nature recycles its good ideas.
Flagship systems
CBASS
Cyclic oligonucleotide-Based Anti-phage Signaling System. The most studied system. Sensor = CD-NTase (a cyclase producing cGAMP/c-di-AMP/etc.). Effector = a Cap (1, 2, 3, or 4) that suicides the bacterium when the second messenger rises. Characterized by Lowey et al., Cell 2020. Why it is valuable: CBASS shares mechanisms with human cGAS-STING. Anti-cancer STING agonists could emerge from here.
Pycsar
Pyrimidine cyclase system for anti-phage resistance. Like CBASS but with cyclic mononucleotides (cCMP, cUMP) instead of dinucleotides. Effector = a TIR (Toll-Interleukin Receptor) domain, with NADase activity. Why it is valuable: the human TIR domain (SARM1) kills axons when activated. Modulators of bacterial TIR therefore shed light on human neuropathies. Characterized by Tal et al., Nature 2021.
RADAR
Restriction by an Adenosine Deaminase Acting on RNA. Sensor = RdrA (ATPase). Effector = RdrB (A→I deaminase on phage double-stranded RNA). Characterized by Duncan-Lowey et al., Cell 2023. Why it is valuable: RdrB is the functional homolog of human ADAR1 (which edits endogenous RNA to prevent self-attack). Targeting ADAR1 = major anti-tumor potential.
Schlafen (bacterial)
A protein that cleaves phage tRNA: without tRNA, there is no translation, and no phage. Why it is valuable: the human paralog SLFN11 is a tumor suppressor that sensitizes cancer cells to topoisomerase chemotherapies. If we learn to activate SLFN11, we make chemoresistance reversible.
Viperin (bacterial)
A Radical-SAM enzyme that produces ddhCTP/ddhGTP. These molecules are nucleotide analogues that terminate the chain when the viral RNA polymerase attempts to incorporate them. Why it is valuable: human RSAD2 (“Viperin”) does the same thing against flaviviruses, HIV, and some coronaviruses. Chemically stabilized ddhCTP = a broad-spectrum natural antiviral. Characterized by Bernheim et al., Nature 2021.
Cross-cutting concepts
Host-directed therapy
Targeting a human protein instead of a viral protein. More robust against viral mutations (the virus mutates, the human does not), but riskier regarding toxicity (we touch our own machinery). The RADAR/ADAR1 and Schlafen/SLFN11 leads are host-directed.
Phage anti-defense
For each bacterial defense, some phages have crafted the counter: a small gene encoding a protein that inhibits the defense. Anti-CRISPRs (Acr) are the best known. There are also Acb1/2/3 (anti-CBASS), Apyc1 (anti-Pycsar)… Why it is valuable: these anti-defenses are natural inhibitors optimized by evolution. They are free reference chemistries. See chapter 6.
Operon defense island
An area of the bacterial genome where multiple defense systems are clustered together. Most bacteria have 5 to 15 different systems in a single genome. Defense Finder and PADLOC are the two bioinformatic tools that detect them. It is the genome’s equivalent of an armory—all the weapons in one place.
A→I editing
A chemical modification that transforms an A (adenosine) into an I (inosine) in RNA. Since inosine is read as a G by the cellular machinery, it changes the codon’s meaning. This is the trick of RADAR (on viral RNA) and ADAR1 (on endogenous RNA, to mask it).
Radical-SAM
An enzyme superfamily that uses S-adenosyl-methionine and a [4Fe-4S] iron-sulfur cluster to perform radical chemistry (= with unpaired electrons). Very weird, very effective, heavily used by Viperins.
Fold
The three-dimensional shape adopted by a protein. Two proteins can have very different sequences and a nearly identical fold (= they probably do the same thing, and often descend from a common distant ancestor). Detected by DALI or Foldseek. It is the compass of cross-kingdom analogy: if a bacterial protein and a human protein share a fold, one can often transfer an inhibitor from one to the other.
RMSD
Root-Mean-Square Deviation. The average distance between two superimposed 3D structures, in angstroms (Å). 0–2 Å = essentially identical structures. 2–4 Å = same fold but some loops diverge. >5 Å = either you are comparing poorly, or they are not the same fold.
Little mental tools
Could you patent the sun?
Jonas Salk’s phrase in 1955 when asked why he did not patent his polio vaccine. It is also our motto. Living things belong to no one. See the landing page.
TAZ
Temporary Autonomous Zone. Hakim Bey’s concept (1991): creating spaces of freedom that ask permission from no one, even briefly. In the Bactaegion version: zero recurring infrastructure cost, hosted for free, ready to disappear cleanly. No authorization needed to exist.
BYOK
Bring Your Own Key. You bring your LLM API key (Claude, GPT, Gemini, or local Ollama). Bactaegion stores nothing and pays nothing for your inference. See /onboarding/.
DID
Decentralized Identifier. A cryptographic identity generated on your device (Touch ID, Windows Hello), which does not depend on a server account. You sign your contributions, you receive your Open Badges 3.0 badges, and no one can confiscate it from you. See /identite/.
To go further
If you want to delve deeper into a concept:
- Chapter 1 · Arms race
- Chapter 2 · The language of cycles (on CBASS / Pycsar)
- Chapter 5 · Silent editing (on RADAR)
- Chapter 6 · When the phage answers (on anti-defenses)
- Daily booster — to pick a concrete question
And if you find a word this glossary does not cover, open a GitHub issue. It is the work of gnomes—and we explicitly recognize it.