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-# Get started
-
-Let's get started with Docus.
-
-# Welcome to Docus
-
-Your new favorite way to build **documentation**.
-
-## How to use Docus ?
-
-Learn more on [docus.dev](https://docus.dev).
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-title: Guide
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+---
+title: Introduction
+---
+
+# Introduction
+
+Bacteriophages, or phages for short, are viruses that infect bacteria and hijack bacterial cellular machinery to reproduce themselves. Phages are extremely abundant entities, and could be responsible for up to 20-40% of bacterial mortality daily (Hampton et al., 2020). Therefore, phage infection constitutes a very strong evolutionary pressure for bacteria.
+
+In response to this evolutionary pressure, bacteria have developed an arsenal of anti-phage defense systems. The term "defense system" here designates either a single gene or a set of genes, which expression provides the bacteria with some level of resistance against phage infection.
+
+# History
+
+The first anti-phage defense system was discovered in the early 1950s by two separate teams of researchers (Luria and Human, 1952 ; Bertani and Wiegle 1952). Luria and Human reported a mysterious phenomenon, where one phage was only capable of infecting a specific bacterial strain once. The progeny phages produced by this first round of infection had lost their ability to infect the same strain again, yet remained able to infect other bacterial strains. For them, this could only mean that "the genotype of the host in which a virus reproduces affects the phenotype of the new virus" (Luria and Human, 1952). A similar phenomenon was shortly after described by Bertani and Wiegle.
+
+Their work was in fact the first report of what would later be named Restriction-Modification ([RM](/list_defense_systems/RM)) system, which is considered to be the first anti-phage defense system discovered.
+
+The sighting of a second defense system occured more than 40 years later, in the late 1980s, when several teams around the world observed arrays containing short, palindromic DNA repeats clustered together on the bacterial genome (Barrangou et al., 2017). Yet, the biological function of these repeats was only elucidated in 2007, when a team of researchers demonstrated that these repeats were part of a new anti-phage defense systems (Barrangou et al., 2007) , known as [CRISPR-Cas system](/list_defense_systems/CRISPR).
+
+Following these two major breakthroughs, knowledge of anti-phage systems remained scarce for some years. Yet, in 2011, Makarova and colleagues revealed that anti-phage systems tend to colocalize on the bacterial genome in defense-islands. This led to a guilt-by-association hypothesis : if a gene or a set of genes is frequently found in bacterial genomes in close proximity to known defense systems, such as RM or CRISPR-Cas systems, then it might constitute a new defense system. This concept had a large role in the discovery of an impressive diversity of defense systems in a very short amount of time. To date, more than 60 defense systems have been described.
+
+## List of known defense systems
+
+To date, more than 60 anti-phage defense systems have been described. An exhaustive list of the systems with experimentally validated anti-phage activity can be found [here](/defense_systems).
+
+## Molecular mechanisms
+
+The molecular mechanisms responsible for the anti-phage activity of defense systems are diverse. Overall, these molecular mechanisms can be divided into 3 categories (Tal and Sorek, 2022):
+
+- **Degrading phage nucleic acids (either DNA or RNA)**
+
+One or a combination of enzymes will degrade phage nucleic acids upon their injection into the bacterial host.
+
+Target nucleic acid recognition and degradation of the target (often through endonuclease activity) are key functions performed by these defense systems. To avoid collateral damage to the bacterial DNA, these functions are accompanied by mechanisms allowing Self versus Non-Self discrimination.
+
+[RM](/list_defense_systems/RM) and [CRISPR-Cas](/list_defense_systems/CRISPR) systems are the main representants of this type of anti-phage systems.
+
+- **Inhibiting nucleic acid synthesis**
+
+After phage nucleic acids are injected, their replication and/or transcription is inhibited.
+
+This can be achieved by the bacteria through the production of small anti-phage molecules (see [Chemical defense](/general_concepts/Chemical_defense)). For instance, [prokaryotic viperins](/list_defense_systems/viperins) produce chain terminators which, once integrated in a nascent nucleic acid, stop its further elongation.
+
+Another possible strategy is the depletion of cell components essential to viral replication. For instance, some enzymes (like dGTPase) deplete the cytosolic pool of deoxynucleotide triphosphates (dNTPs), which are essential building blocks for nucleic acid synthesis.
+
+- **Abortive infection**
+
+Abortive infection can be described as the suicide of a bacteria when infected by a phage. The premature death of the bacterial host prevents the completion of the phage infection cycle, therefore avoiding the production and release of a multitude of newly formed phages. This represents a widespread strategy for anti-phage defense at the community level in bacterial populations.
+
+Abortive infection usually involves a sensor module responsible for detecting phage infection and activating an effector module, which will in turn mediates cell death.
+
+## Impact and applications of defense systems in diverse fields
+
+The study of anti-phage defense systems has had a significant impact on a striking amount of research and industry fields:
+
+- **molecular biology**
+
+The discovery of the first anti-phage system also marked the discovery of restriction enzymes, which are key elements of RM systems. Through their ability to recognize specific nucleic sequences and cleave nucleic acid, restriction enzymes quickly became invaluable tools for molecular biology. A Nobel Prize was awarded in 1978 to Werner Arber, Daniel Nathans and Hamilton O. Smith ["for the discovery of restriction enzymes and their application to problems of molecular genetics."](/https://www.nobelprize.org/prizes/medicine/1978/summary/)
+
+A few decades later, the discovery of CRISPR-Cas systems also created a major genome editing revolution. The Cas nucleases are major components of CRISPR-Cas, and are able to specifically recognize and bind a given nucleic sequence thanks to an RNA guide. This RNA guide can easily be programmed to target any desired sequence, making CRISPR-Cas derived components extremely powerful tools for researchers. A Nobel prize was awarded in 2020 to Emmanuelle Charpentier and Jennifer A. Doudna ["for the development of a method for genome editing"](/https://www.nobelprize.org/prizes/chemistry/2020/summary/).
+
+- **agri-food industries**
+
+- **human health**
+
+## References
+
+Barrangou, R. et al. CRISPR provides acquired resistance against viruses in
+prokaryotes. Science 315, 1709–1712 (2007)
+
+Barrangou R, Horvath P. A decade of discovery: CRISPR functions and applications. Nat Microbiol. 2017 Jun 5;2:17092. doi: 10.1038/nmicrobiol.2017.92. PMID: 28581505
+
+BERTANI, G, and J J WEIGLE. “Host controlled variation in bacterial viruses.†Journal of bacteriology vol. 65,2 (1953): 113-21. doi:10.1128/jb.65.2.113-121.1953
+
+Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R. Systematic discovery of antiphage defense systems in the microbial pangenome. Science. 2018 Mar 2;359(6379):eaar4120. doi: 10.1126/science.aar4120. Epub 2018 Jan 25. PMID: 29371424; PMCID: PMC6387622.
+
+Gao L, Altae-Tran H, Böhning F, et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science. 2020;369(6507):1077-1084. doi:10.1126/science.aba0372
+
+Hampton, H. G., Watson, B. N. J. & Fineran, P. C. The arms race between bacteria and their phage foes. Nature 577, 327–336 (2020)
+
+LURIA SE, HUMAN ML. A nonhereditary, host-induced variation of bacterial viruses. J Bacteriol. 1952;64(4):557-569. doi:10.1128/jb.64.4.557-569.1952
+
+Makarova KS, Wolf YI, Snir S, Koonin EV. Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J Bacteriol. 2011 Nov;193(21):6039-56. doi: 10.1128/JB.05535-11. Epub 2011 Sep 9. PMID: 21908672; PMCID: PMC3194920.
+
+Tal N, Sorek R. SnapShot: Bacterial immunity. Cell. 2022 Feb 3;185(3):578-578.e1. doi: 10.1016/j.cell.2021.12.029. PMID: 35120666.
+
+
diff --git a/content/2.defense-systems/0.index.md b/content/2.defense-systems/0.index.md
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+---
+title: List of defense systems
+---
+
+# List of defense systems
+
+The knowledge of anti-phage defense systems is ever expanding. The spectacular increase of the number of known systems in the past years suggests that many of them are still to be discovered. As of april 2022, 63 defense systems have been described.
+
+| | |
+| ------------------------------------------ | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **System** | **Article** |
+| Abi2 | Chopin, M.-C., Chopin, A., Bidnenko, E., 2005. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473–479. [https://doi.org/10.1016/j.mib.2005.06.006](https://doi.org/10.1016/j.mib.2005.06.006) |
+| [AbiE](/defense-systems/abie) | Dy, R.L., Przybilski, R., Semeijn, K., Salmond, G.P.C., Fineran, P.C., 2014. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res 42, 4590–4605. [https://doi.org/10.1093/nar/gkt1419](https://doi.org/10.1093/nar/gkt1419) |
+| AbiH | Prévots, F., Daloyau, M., Bonin, O., Dumont, X., Tolou, S., 1996. Cloning and sequencing of the novel abortive infection gene abiH of Lactococcus lactis ssp. lactis biovar. diacetylactis S94. FEMS Microbiol Lett 142, 295–299. [https://doi.org/10.1111/j.1574-6968.1996.tb08446.x](https://doi.org/10.1111/j.1574-6968.1996.tb08446.x) |
+| Ago | Garb, J. _et al._ _Multiple phage resistance systems inhibit infection via SIR2-dependent NAD + depletion_. (2021). doi:10.1101/2021.12.14.472415.<br><br>Zeng Z, Chen Y, Pinilla-Redondo R, Shah SA, Zhao F, Wang C, Hu Z, Wu C, Zhang C, Whitaker RJ, She Q, Han W. A short prokaryotic Argonaute activates membrane effector to confer antiviral defense. Cell Host Microbe. 2022 Jul 13;30(7):930-943.e6. doi: 10.1016/j.chom.2022.04.015. Epub 2022 May 19. PMID: 35594868. |
+| [AVAST](/list_defense_systems/AVAST) | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| [BREX](/list_defense_systems/BREX) | Goldfarb, T., Sberro, H., Weinstock, E., Cohen, O., Doron, S., Charpak-Amikam, Y., Afik, S., Ofir, G., Sorek, R., 2015. BREX is a novel phage resistance system widespread in microbial genomes. The EMBO Journal 34, 169–183. [https://doi.org/10.15252/embj.201489455](https://doi.org/10.15252/embj.201489455) |
+| [BstA](/list_defense_systems/BstA) | Owen, S.V., Wenner, N., Dulberger, C.L., Rodwell, E.V., Bowers-Barnard, A., Quinones-Olvera, N., Rigden, D.J., Rubin, E.J., Garner, E.C., Baym, M., Hinton, J.C.D., 2020. Prophage-encoded phage defence proteins with cognate self-immunity. bioRxiv 2020.07.13.199331. [https://doi.org/10.1101/2020.07.13.199331](https://doi.org/10.1101/2020.07.13.199331) |
+| Cas | Bernheim, A., Bikard, D., Touchon, M., Rocha, E.P.C., 2020. Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements. Nucleic Acids Res 48, 748–760. [https://doi.org/10.1093/nar/gkz1091](https://doi.org/10.1093/nar/gkz1091) |
+| CBASS | Millman, A., Melamed, S., Amitai, G., Sorek, R., 2020. Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems. Nature Microbiology 5, 1608–1615. [https://doi.org/10.1038/s41564-020-0777-y](https://doi.org/10.1038/s41564-020-0777-y) |
+| DarTG | LeRoux, M., Srikant, S., Littlehale, M.H., Teodoro, G., Doron, S., Badiee, M., Leung, A.K.L., Sorek, R., Laub, M.T., 2021. The DarTG toxin-antitoxin system provides phage defense by ADP-ribosylating viral DNA. bioRxiv 2021.09.27.462013. [https://doi.org/10.1101/2021.09.27.462013](https://doi.org/10.1101/2021.09.27.462013) |
+| dCTPdeaminase | Tal, N., Millman, A., Stokar-Avihail, A., Fedorenko, T., Leavitt, A., Melamed, S., Yirmiya, E., Avraham, C., Amitai, G., Sorek, R., 2021. Antiviral defense via nucleotide depletion in bacteria. bioRxiv 2021.04.26.441389. [https://doi.org/10.1101/2021.04.26.441389](https://doi.org/10.1101/2021.04.26.441389) |
+| dGTPase | Tal, N., Millman, A., Stokar-Avihail, A., Fedorenko, T., Leavitt, A., Melamed, S., Yirmiya, E., Avraham, C., Amitai, G., Sorek, R., 2021. Antiviral defense via nucleotide depletion in bacteria. bioRxiv 2021.04.26.441389. [https://doi.org/10.1101/2021.04.26.441389](https://doi.org/10.1101/2021.04.26.441389) |
+| DISARM | Ofir, G., Melamed, S., Sberro, H., Mukamel, Z., Silverman, S., Yaakov, G., Doron, S., Sorek, R., 2018. DISARM is a widespread bacterial defence system with broad anti-phage activities. Nat Microbiol 3, 90–98. [https://doi.org/10.1038/s41564-017-0051-0](https://doi.org/10.1038/s41564-017-0051-0) |
+| Dnd | Wang, L., Chen, S., Xu, T., Taghizadeh, K., Wishnok, J.S., Zhou, X., You, D., Deng, Z., Dedon, P.C., 2007. Phosphorothioation of DNA in bacteria by dnd genes. Nat Chem Biol 3, 709–710. [https://doi.org/10.1038/nchembio.2007.39](https://doi.org/10.1038/nchembio.2007.39) |
+| DRT | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| Druantia | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+| Dsr | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| [Gabija](/list_defense_systems/Gabija) | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+| Gao_ApeA | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| Gao_Her | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| Gao_Hhe | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| Gao_Iet | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| Gao_Mza | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| Gao_Ppl | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| Gao_Qat | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| Gao_RL | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| Gao_TerYP | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| Gao_Tmn | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| Gao_Upx | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| GasderMIN | Johnson, A.G., Wein, T., Mayer, M.L., Duncan-Lowey, B., Yirmiya, E., Oppenheimer-Shaanan, Y., Amitai, G., Sorek, R., Kranzusch, P.J., 2021. Bacterial gasdermins reveal an ancient mechanism of cell death. bioRxiv 2021.06.07.447441. [https://doi.org/10.1101/2021.06.07.447441](https://doi.org/10.1101/2021.06.07.447441) |
+| [Hachiman](/list_defense_systems/Hachiman) | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+| Kiwa | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+| [Lamassu](/list_defense_systems/Lamassu) | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+| Lit | Uzan, M., Miller, E.S., 2010. Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation. Virology Journal 7, 360. [https://doi.org/10.1186/1743-422X-7-360](https://doi.org/10.1186/1743-422X-7-360) |
+| Nhi | Bari, S.M.N., Chou-Zheng, L., Cater, K., Dandu, V.S., Thomas, A., Aslan, B., Hatoum-Aslan, A., 2019. A unique mode of nucleic acid immunity performed by a single multifunctional enzyme. bioRxiv 776245. [https://doi.org/10.1101/776245](https://doi.org/10.1101/776245) |
+| NixI | LeGault, K.N., Barth, Z.K., DePaola, P., Seed, K.D., 2021. A phage parasite deploys a nicking nuclease effector to inhibit replication of its viral host. bioRxiv 2021.07.12.452122. [https://doi.org/10.1101/2021.07.12.452122](https://doi.org/10.1101/2021.07.12.452122) |
+| [PARIS](/list_defense_systems/PARIS) | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
+| Pif | Cram, D., Ray, A., Skurray, R., 1984. Molecular analysis of F plasmid pif region specifying abortive infection of T7 phage. Mol Gen Genet 197, 137–142. [https://doi.org/10.1007/BF00327934](https://doi.org/10.1007/BF00327934) |
+| PrrC | Uzan, M., Miller, E.S., 2010. Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation. Virology Journal 7, 360. [https://doi.org/10.1186/1743-422X-7-360](https://doi.org/10.1186/1743-422X-7-360) |
+| [RADAR](/list_defense_systems/RADAR) | Gao, L., Altae-Tran, H., Böhning, F., Makarova, K.S., Segel, M., Schmid-Burgk, J.L., Koob, J., Wolf, Y.I., Koonin, E.V., Zhang, F., 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084. [https://doi.org/10.1126/science.aba0372](https://doi.org/10.1126/science.aba0372) |
+| Retron | Mestre, M.R., González-Delgado, A., Gutiérrez-Rus, L.I., MartÃnez-Abarca, F., Toro, N., 2020. Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems. Nucleic Acids Res 48, 12632–12647. [https://doi.org/10.1093/nar/gkaa1149](https://doi.org/10.1093/nar/gkaa1149) <br><br>Millman, A., Bernheim, A., Stokar-Avihail, A., Fedorenko, T., Voichek, M., Leavitt, A., Oppenheimer-Shaanan, Y., Sorek, R., 2020. Bacterial Retrons Function In Anti-Phage Defense. Cell 183, 1551-1561.e12. [https://doi.org/10.1016/j.cell.2020.09.065](https://doi.org/10.1016/j.cell.2020.09.065) |
+| RexAB | Parma, D.H., Snyder, M., Sobolevski, S., Nawroz, M., Brody, E., Gold, L., 1992. The Rex system of bacteriophage lambda: tolerance and altruistic cell death. Genes Dev 6, 497–510. [https://doi.org/10.1101/gad.6.3.497](https://doi.org/10.1101/gad.6.3.497) |
+| [RM](/defense_systems/RM) | Oliveira, P.H., Touchon, M., Rocha, E.P.C., 2014. The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts. Nucleic Acids Research 42, 10618. [https://doi.org/10.1093/nar/gku734](https://doi.org/10.1093/nar/gku734) |
+| Rst_2TM_1TM_TIR | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
+| Rst_3HP | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
+| Rst_DprA-PPRT | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
+| Rst_DUF4238 | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
+| Rst_gop_beta_cll | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
+| Rst_HelicaseDUF2290 | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
+| Rst_Hydrolase-Tm | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
+| Rst_Old_Tin | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
+| Rst_Retron-Tm | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
+| Rst_TIR | Rousset, F., Dowding, J., Bernheim, A., Rocha, E.P.C., Bikard, D., 2021. Prophage-encoded hotspots of bacterial immune systems. bioRxiv 2021.01.21.427644. [https://doi.org/10.1101/2021.01.21.427644](https://doi.org/10.1101/2021.01.21.427644) |
+| Septu | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+| Shedu | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+| SspBCDE | Wang, S., Wan, M., Huang, R., Zhang, Y., Xie, Y., Wei, Y., Ahmad, M., Wu, D., Hong, Y., Deng, Z., Chen, S., Li, Z., Wang, L., n.d. SspABCD-SspFGH Constitutes a New Type of DNA Phosphorothioate-Based Bacterial Defense System. mBio 12, e00613-21. [https://doi.org/10.1128/mBio.00613-21](https://doi.org/10.1128/mBio.00613-21) |
+| Stk2 | Depardieu, F., Didier, J.-P., Bernheim, A., Sherlock, A., Molina, H., Duclos, B., Bikard, D., 2016. A Eukaryotic-like Serine/Threonine Kinase Protects Staphylococci against Phages. Cell Host & Microbe 20, 471–481. [https://doi.org/10.1016/j.chom.2016.08.010](https://doi.org/10.1016/j.chom.2016.08.010) |
+| [Thoeris](/list_defense_systems/Thoeris) | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+| [Viperin](/list_defense_systems/viperins) | Bernheim, A., Millman, A., Ofir, G., Meitav, G., Avraham, C., Shomar, H., Rosenberg, M.M., Tal, N., Melamed, S., Amitai, G., Sorek, R., 2021. Prokaryotic viperins produce diverse antiviral molecules. Nature 589, 120–124. [https://doi.org/10.1038/s41586-020-2762-2](https://doi.org/10.1038/s41586-020-2762-2) |
+| Wadjet | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+| Zorya | Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., Sorek, R., 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359. [https://doi.org/10.1126/science.aar4120](https://doi.org/10.1126/science.aar4120) |
+
+**From** **_Tesson et al., 2022_**
+
+## References
+
+Florian Tesson, Alexandre Hervé, Marie Touchon, Camille d’Humières, Jean Cury, Aude Bernheim, bioRxiv 2021.09.02.458658; doi: https://doi.org/10.1101/2021.09.02.458658
diff --git a/content/2.defense-systems/1.PARIS.md b/content/2.defense-systems/1.PARIS.md
new file mode 100644
index 0000000000000000000000000000000000000000..449053c8cebb3411674e40281f69faf1b1f0e690
--- /dev/null
+++ b/content/2.defense-systems/1.PARIS.md
@@ -0,0 +1,76 @@
+---
+title: Paris
+toc: true
+---
+
+# PARIS system
+
+PARIS (for Phage Anti-Restriction-Induced System) is a novel anti-phage system. PARIS is found in 4% of prokaryotic genomes. It comprises an ATPase associated with a DUF4435 protein, which can be found either as a two-gene cassette or a single-gene fusion (1).
+
+This system relies on an unknown [Abortive infection](/general_concepts/Abi) mechanism to trigger growth arrest upon sensing a phage-encoded protein (Ocr). Interestingly, the Ocr protein has been found to inhibit R-M systems and BREX systems, making PARIS a suitable defense mechanism against RM resistant and/or BREX resistant phages (1, 2, 3).
+
+## Relevant abstracts
+
+**François Rousset, Julien Dowding, Aude Bernheim, Eduardo P.C. Rocha, David Bikard, Prophage-encoded hotspots of bacterial immune systems, bioRxiv 2021.01.21.427644; doi: https://doi.org/10.1101/2021.01.21.427644**
+
+The arms race between bacteria and phages led to the emergence of a variety of genetic systems used by bacteria to defend against viral infection, some of which were repurposed as powerful biotechnological tools. While numerous defense systems have been identified in genomic regions termed defense islands, it is believed that many more remain to be discovered. Here, we show that P2- like prophages and their P4-like satellites have genomic hotspots that represent a significant source of novel anti-phage systems. We validate the defense activity of 14 systems spanning various protein domains and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein. Immunity hotspots are present across prophages of distant bacterial species, highlighting their biological importance in the competition between bacteria and phages.
+
+## Example of genomic structure
+
+There is 2 types of PARIS systems:
+
+### Paris type I
+
+::card
+#title
+Paris type I : AriA*I Â (AAA*15) + AriB (DUF4435) or AriAB (fused AAA_15 + DUF4435)
+
+#description
+
+::
+
+<br/>
+
+::card
+#title
+Paris type I system in _Salmonella enterica_ (GCF\__000006945.2). AriA_I:_ NP_461673.1; AriB: NP_461674.1
+
+#description
+
+::
+
+<br/>
+
+::card
+#title
+Paris type I merge system in _Sideroxydans lithotrophicus_ (GCF\__000025705.1). AriAB_I:_ WP_013030315.1
+::
+
+### Paris type II
+
+2\. Paris type II : AriAB (AAA\__21) + AriB (DUF4435) or AriAB (fused AAA_21 + DUF4435)_
+
+
+
+Paris type II system in *Escherichia coli*Â (GCF_000026245.1*). AriA_II:* WP_000190961.1 ; AriB: WP_000134255.1
+
+
+
+Paris type II merge system in _Desulfovibrio desulfuricans_ (GCF\__000025705.1). AriAB_I:_ WP_209818471.1
+
+## ReferencesÂ
+
+1. François Rousset, Julien Dowding, Aude Bernheim, Eduardo P.C. Rocha, David Bikard, Prophage-encoded hotspots of bacterial immune systems, bioRxiv 2021.01.21.427644; doi: https://doi.org/10.1101/2021.01.21.427644
+
+2. Isaev A, Drobiazko A, Sierro N, et al. Phage T7 DNA mimic protein Ocr is a potent inhibitor of BREX defence \[published correction appears in Nucleic Acids Res. 2020 Jul 27;48(13):7601-7602\]. _Nucleic Acids Res_. 2020;48(10):5397-5406. doi:10.1093/nar/gkaa290
+
+3. Studier FW. Gene 0.3 of bacteriophage T7 acts to overcome the DNA restriction system of the host. J Mol Biol. 1975 May 15;94(2):283-95. doi: 10.1016/0022-2836(75)90083-2. PMID: 1095770.
+
+::references-list
+---
+items:
+ - 10.1101/2021.01.21.427644
+ - 10.1093/nar/gkaa290
+ - 10.1016/0022-2836(75)90083-2
+---
+::
\ No newline at end of file
diff --git a/content/2.defense-systems/2.AbiE.md b/content/2.defense-systems/2.AbiE.md
new file mode 100644
index 0000000000000000000000000000000000000000..633777a57803ae76da6cedacd5b9e67568a862b7
--- /dev/null
+++ b/content/2.defense-systems/2.AbiE.md
@@ -0,0 +1,99 @@
+---
+title: AbiE
+---
+
+# AbiE system
+
+AbiE is a family of an anti-phage defense systems. They act through a Toxin-Antitoxin mechanism, and are comprised of a pair of genes, with one gene being toxic while the other confers immunity to this toxicity.
+
+It is classified as an [Abortive infection](/general_concepts/Abi) system.
+
+## Mechanism
+
+AbiE systems are encoded by two mandatory genes, abiEi and abiEii (1,2).  The latter encodes for AbiEii, a GTP-binding nucleotidyltransferase (NTase) which expression induce a reversible growth arrest.  On the other hand, abiEi encodes for a AbiEi a transcriptional autorepressor that  binds to the promoter of the abiE operon.
+
+Based on this mechanisms, AbiE systems are classified as Type IV Toxin-Antitoxin system, where the antitoxin and toxin are both proteins that do not directly interact with each other.
+
+## Relevant Abstracts
+
+
+::card{icon="ooui:article-ltr"}
+#title
+Garvey P, Fitzgerald GF, Hill C. Cloning and DNA sequence analysis of two abortive infection phage resistance determinants from the lactococcal plasmid pNP40. Appl Environ Microbiol. 1995 Dec;61(12):4321-8. doi: 10.1128/aem.61.12.4321-4328.1995. PMID: 8534099; PMCID: PMC167743.
+#description
+The lactococcal plasmid pNP40, from Lactococcus lactis subsp. lactis biovar diacetylactis DRC3, confers complete resistance to the prolate-headed phage phi c2 and the small isometric-headed phage phi 712 in L. lactis subsp. lactis MG1614. A 6.0-kb NcoI fragment of pNP40 cloned in the lactococcal Escherichia coli shuttle vector pAM401 was found to confer partial resistance to phi 712. Subcloning and deletion analysis of the recombinant plasmid pPG01 defined a 2.5-kb ScaIHpaI fragment as conferring phage insensitivity. Sequence analysis of this region confirmed the presence of two overlapping open reading frames (ORFs). Further subcloning of pNP40 to characterize the resistance determinant active against phi c2 identified a 5.6-kb EcoRV fragment of pNP40 which, when cloned in pAM401, conferred partial resistance to both phi c2 and phi 712. Subcloning and deletion analysis of the recombinant plasmid pCG1 defined a 3.7-kb EcoRV-XbaI fragment as encoding phage insensitivity. DNA sequence analysis of this region revealed the presence of a single complete ORF. The introduction of a frameshift mutation at the unique BglII site within this ORF disrupted the phage resistance phenotype, confirming that this ORF is responsible for the observed phage insensitivity. The mechanisms encoded by pPG01 and pCG1 in L. lactis subsp. lactis MG1614 conformed to the criteria defining abortive infection and were designated AbiE and AbiF, respectively. Analysis of the phage DNA content of phi 712-infected hosts containing AbiF demonstrated that it inhibited the rate of phage DNA replication, while AbiE had little effect on phage DNA replication, suggesting a later target of inhibition. The predicted protein product of abiF shows significant homology to the products of two other lactococcal abortive infection genes, abiD and abiD1
+::
+
+<br/>
+
+::card{icon="ooui:article-ltr"}
+#title
+Tangney M, Fitzgerald GF. Effectiveness of the lactococcal abortive infection systems AbiA, AbiE, AbiF and AbiG against P335 type phages. FEMS Microbiol Lett. 2002 Apr 23;210(1):67-72. doi: 10.1111/j.1574-6968.2002.tb11161.x. PMID: 12023079.
+#description
+Four lactococcal abortive infection mechanisms were introduced into strains which were sensitive hosts for P335 type phages and plaque assay experiments performed to assess their effect on five lactococcal bacteriophages from this family. Results indicate that AbiA inhibits all five P335 phages tested, while AbiG affects φP335 itself and φQ30 but not the other P335 species phages. AbiA was shown to retard phage Q30 DNA replication as previously reported for other phages. It was also demonstrated that AbiG, previously shown to act at a point after DNA replication in the cases of c2 type and 936 type phages, acts at the level of, or prior to phage Q30 DNA replication. AbiE and AbiF had no effect on the P335 type phages examined.
+::
+
+<br/>
+
+::card{icon="ooui:article-ltr"}
+#title
+Dy RL, Przybilski R, Semeijn K, Salmond GP, Fineran PC. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res. 2014;42(7):4590-4605. doi:10.1093/nar/gkt1419
+#description
+Bacterial abortive infection (Abi) systems are ‘altruistic’ cell death systems that are activated by phage infection and limit viral replication, thereby providing protection to the bacterial population. Here, we have used a novel approach of screening Abi systems as a tool to identify and characterize toxin–antitoxin (TA)-acting Abi systems. We show that AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism. The abiE operon was negatively autoregulated by the antitoxin, AbiEi, a member of a widespread family of putative transcriptional regulators. AbiEi has an N-terminal winged-helix-turn-helix domain that is required for repression of abiE transcription, and an uncharacterized bi-functional C-terminal domain, which is necessary for transcriptional repression and sufficient for toxin neutralization. The cognate toxin, AbiEii, is a predicted nucleotidyltransferase (NTase) and member of the DNA polymerase β family. AbiEii specifically bound GTP, and mutations in conserved NTase motifs (I-III) and a newly identified motif (IV), abolished GTP binding and subsequent toxicity. The AbiE systems can provide phage resistance and enable stabilization of mobile genetic elements, such as plasmids. Our study reveals molecular insights into the regulation and function of the widespread bi-functional AbiE Abi-TA systems and the biochemical properties of both toxin and antitoxin proteins
+::
+
+<br/>
+
+::card{icon="ooui:article-ltr"}
+#title
+Li Z, Song Q, Wang Y, Xiao X, Xu J. Identification of a functional toxin-antitoxin system located in the genomic island PYG1 of piezophilic hyperthermophilic archaeon Pyrococcus yayanosii. Extremophiles. 2018 May;22(3):347-357. doi: 10.1007/s00792-018-1002-2. Epub 2018 Jan 15. PMID: 29335804.
+
+#description
+Toxin-antitoxin (TA) system is bacterial or archaeal genetic module consisting of toxin and antitoxin gene that be organized as a bicistronic operon. TA system could elicit programmed cell death, which is supposed to play important roles for the survival of prokaryotic population under various physiological stress conditions. The phage abortive infection system (AbiE family) belongs to bacterial type IV TA system. However, no archaeal AbiE family TA system has been reported so far. In this study, a putative AbiE TA system (PygAT), which is located in a genomic island PYG1 in the chromosome of Pyrococcus yayanosii CH1, was identified and characterized. In Escherichia coli, overexpression of the toxin gene pygT inhibited its growth while the toxic effect can be suppressed by introducing the antitoxin gene pygA in the same cell. PygAT also enhances the stability of shuttle plasmids with archaeal plasmid replication protein Rep75 in E. coli. In P. yayanosii, disruption of antitoxin gene pygA cause a significantly growth delayed under high hydrostatic pressure (HHP). The antitoxin protein PygA can specifically bind to the PygAT promoter region and regulate the transcription of pygT gene in vivo. These results show that PygAT is a functional TA system in P. yayanosii, and also may play a role in the adaptation to HHP environment.
+::
+
+<br/>
+
+::card{icon="ooui:article-ltr"}
+#title
+Hampton HG, Jackson SA, Fagerlund RD, Vogel AIM, Dy RL, Blower TR, Fineran PC. AbiEi Binds Cooperatively to the Type IV abiE Toxin-Antitoxin Operator Via a Positively-Charged Surface and Causes DNA Bending and Negative Autoregulation. J Mol Biol. 2018 Apr 13;430(8):1141-1156. doi: 10.1016/j.jmb.2018.02.022. Epub 2018 Mar 6. PMID: 29518409.
+
+#description
+Bacteria resist phage infection using multiple strategies, including CRISPR-Cas and abortive infection (Abi) systems. Abi systems provide population-level protection from phage predation, via "altruistic" cell suicide. It has recently been shown that some Abi systems function via a toxin-antitoxin mechanism, such as the widespread AbiE family. The Streptococcus agalactiae AbiE system consists of a bicistronic operon encoding the AbiEi antitoxin and AbiEii toxin, which function as a Type IV toxin-antitoxin system. Here we examine the AbiEi antitoxin, which belongs to a large family of transcriptional regulators with a conserved N-terminal winged helix-turn-helix domain. This winged helix-turn-helix is essential for transcriptional repression of the abiE operon. The function of the AbiEi C-terminal domain is poorly characterized, but it contributes to transcriptional repression and is sufficient for toxin neutralization. We demonstrate that a conserved charged surface on one face of the C-terminal domain assists sequence-specific DNA binding and negative autoregulation, without influencing antitoxicity. Furthermore, AbiEi binds cooperatively to two inverted repeats within the abiE promoter and bends the DNA by 72°. These findings demonstrate that the mechanism of DNA binding by the widespread family of AbiEi antitoxins and transcriptional regulators can contribute to negative autoregulation
+::
+
+<br/>
+
+::card{icon="ooui:article-ltr"}
+#title
+Beck IN, Usher B, Hampton HG, Fineran PC, Blower TR. Antitoxin autoregulation of M. tuberculosis toxin-antitoxin expression through negative cooperativity arising from multiple inverted repeat sequences. Biochem J. 2020 Jun 26;477(12):2401-2419. doi: 10.1042/BCJ20200368. PMID: 32519742; PMCID: PMC7319586.
+
+#description
+Toxin-antitoxin systems play key roles in bacterial adaptation, including protection from antibiotic assault and infection by bacteriophages. The type IV toxin-antitoxin system AbiE encodes a DUF1814 nucleotidyltransferase-like toxin, and a two-domain antitoxin. In Streptococcus agalactiae, the antitoxin AbiEi negatively autoregulates abiE expression through positively co-operative binding to inverted repeats within the promoter. The human pathogen Mycobacterium tuberculosis encodes four DUF1814 putative toxins, two of which have antitoxins homologous to AbiEi. One such M. tuberculosis antitoxin, named Rv2827c, is required for growth and whilst the structure has previously been solved, the mode of regulation is unknown. To complete the gaps in our understanding, we first solved the structure of S. agalactiae AbiEi to 1.83 Å resolution for comparison with M. tuberculosis Rv2827c. AbiEi contains an N-terminal DNA binding domain and C-terminal antitoxicity domain, with bilateral faces of opposing charge. The overall AbiEi fold is similar to Rv2827c, though smaller, and with a 65° difference in C-terminal domain orientation. We further demonstrate that, like AbiEi, Rv2827c can autoregulate toxin-antitoxin operon expression. In contrast with AbiEi, the Prv2827c promoter contains two sets of inverted repeats, which bind Rv2827c with differing affinities depending on the sequence consensus. Surprisingly, Rv2827c bound with negative co-operativity to the full Prv2827c promoter, demonstrating an unexpectedly complex form of transcriptional regulation.
+::
+
+<br/>
+
+::card{icon="ooui:article-ltr"}
+#title
+Hampton HG, Smith LM, Ferguson S, Meaden S, Jackson SA, Fineran PC. Functional genomics reveals the toxin-antitoxin repertoire and AbiE activity in Serratia. Microb Genom. 2020 Nov;6(11):mgen000458. doi: 10.1099/mgen.0.000458. PMID: 33074086; PMCID: PMC7725324.\*\*
+
+#description
+Bacteriophage defences are divided into innate and adaptive systems. Serratia sp. ATCC 39006 has three CRISPR-Cas adaptive immune systems, but its innate immune repertoire is unknown. Here, we re-sequenced and annotated the Serratia genome and predicted its toxin-antitoxin (TA) systems. TA systems can provide innate phage defence through abortive infection by causing infected cells to 'shut down', limiting phage propagation. To assess TA system function on a genome-wide scale, we utilized transposon insertion and RNA sequencing. Of the 32 TA systems predicted bioinformatically, 4 resembled pseudogenes and 11 were demonstrated to be functional based on transposon mutagenesis. Three functional systems belonged to the poorly characterized but widespread, AbiE, abortive infection/TA family. AbiE is a type IV TA system with a predicted nucleotidyltransferase toxin. To investigate the mode of action of this toxin, we measured the transcriptional response to AbiEii expression. We observed dysregulated levels of tRNAs and propose that the toxin targets tRNAs resulting in bacteriostasis. A recent report on a related toxin shows this occurs through addition of nucleotides to tRNA(s). This study has demonstrated the utility of functional genomics for probing TA function in a high-throughput manner, defined the TA repertoire in Serratia and shown the consequences of AbiE induction.
+::
+
+## Sources
+
+1. Garvey P, Fitzgerald GF, Hill C. Cloning and DNA sequence analysis of two abortive infection phage resistance determinants from the lactococcal plasmid pNP40. Appl Environ Microbiol. 1995 Dec;61(12):4321-8. doi: 10.1128/aem.61.12.4321-4328.1995. PMID: 8534099; PMCID: PMC167743.
+2. Dy RL, Przybilski R, Semeijn K, Salmond GP, Fineran PC. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res. 2014;42(7):4590-4605. doi:10.1093/nar/gkt1419
+
+
+::references-list
+---
+items:
+ - 10.1093/nar/gkt1419
+ - 10.1128/aem.61.12.4321-4328.1995
+---
+::
+
+
diff --git a/content/2.defense-systems/3.AVAST.md b/content/2.defense-systems/3.AVAST.md
new file mode 100644
index 0000000000000000000000000000000000000000..fa0097b73dd96c8f3239ae3e3a52ffc816e62b5e
--- /dev/null
+++ b/content/2.defense-systems/3.AVAST.md
@@ -0,0 +1,18 @@
+# AVAST
+
+AVAST (antiviral ATPases/NTPases of the STAND superfamily) is a group of anti-phage defense systems, active against some dsDNA phages.Â
+
+AVAST systems are composed of NTPases of the STAND (signal transduction ATPases with numerous associated domains) superfamily (1). Â STAND-NTPases typically contain a C-terminal helical sensor domain that activates the N-terminal effector domain upon target recognition (1).
+
+In eukaryotes, STAND-NTPases are associated with programmed cell death, therefore Gao and colleagues hypothesized that AVAST might function through an [Abortive infection mechanism.](/general_concepts/Abi)
+
+## Relevant abstracts
+
+**Gao L, Altae-Tran H, Böhning F, et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes.** ***Science*****. 2020;369(6507):1077-1084. doi:10.1126/science.aba0372**
+
+Bacteria and archaea are frequently attacked by viruses and other mobile genetic elements and rely on dedicated antiviral defense systems, such as restriction endonucleases and CRISPR, to survive. The enormous diversity of viruses suggests that more types of defense systems exist than are currently known. By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. These systems incorporate enzymatic activities not previously implicated in antiviral defense, including RNA editing and retron satellite DNA synthesis. In addition, we computationally predict a diverse set of other putative defense genes that remain to be characterized. These results highlight an immense array of molecular functions that microbes use against viruses.
+
+## References
+
+**1\.** Gao L, Altae-Tran H, Böhning F, et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science. 2020;369(6507):1077-1084. doi:10.1126/science.aba0372
+
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index 0000000000000000000000000000000000000000..24957f0b2727272d7728c3a498f4d5a594db970f
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