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# AVAST
## Description
AVAST (antiviral ATPases/NTPases of the STAND superfamily) is a group of anti-phage defense systems, active against some dsDNA phages.
AVAST systems are composed of NTPases of the STAND (signal transduction ATPases with numerous associated domains) superfamily (1). 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.
## Example of genomic structure
The AVAST system have been describe in a total of 5 subsystems.
Here is some example found in the RefSeq database:
<img src="./data/AVAST_I.svg">
AVAST\_I subsystem in the genome of *Vibrio sp.* (GCF\_905175355.1) is composed of 3 proteins: Avs1A (WP\_208445041.1), Avs1B (WP\_208445042.1)and, Avs1C (WP\_108173272.1).
<img src="./data/AVAST_II.svg">
AVAST\_II subsystem in the genome of *Escherichia coli* (GCF\_018884505.1) is composed of 1 protein: Avs2A (WP\_032199984.1).
<img src="./data/AVAST_III.svg">
AVAST\_III subsystem in the genome of *Enterobacter cancerogenus* (GCF\_002850575.1) is composed of 2 proteins: Avs3B (WP\_199559884.1)and, Avs3A (WP\_101737373.1).
<img src="./data/AVAST_IV.svg">
AVAST\_IV subsystem in the genome of *Escherichia coli* (GCF\_016903595.1) is composed of 1 protein: Avs4A (WP\_000240574.1).
<img src="./data/AVAST_V.svg">
AVAST\_V subsystem in the genome of *Leclercia adecarboxylata* (GCF\_006171285.1) is composed of 1 protein: Avs5A (WP\_139565349.1).
## Distribution of the system among prokaryotes
The AVAST system is present in a total of 363 different species.
Among the 22k complete genomes of RefSeq, this system is present in 1046 genomes (4.6 %).
<img src="./data/Distribution_AVAST.svg" width=800px>
*Proportion of genome encoding the AVAST system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
## Experimental validation
AVAST systems were experimentally validated using:
Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Escherichia coli* has an anti-phage effect against T4, Lambda, HK97, HK544, HK578, T7 (Fillol-Salom et al., 2022)
Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Salmonella enterica * has an anti-phage effect against P22, BTP1, ES18, det7 (Fillol-Salom et al., 2022)
Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Klebsiella pneumoniae * has an anti-phage effect against Pokey (Fillol-Salom et al., 2022)
Subsystem Metallo beta-lactamase + protease + STAND (Type 1) with a system from *Erwinia piriflorinigrans* in *Escherichia coli* has an anti-phage effect against P1 (Gao et al., 2020)
Subsystem STAND (Type 2) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, P1 (Gao et al., 2020)
Subsystem DUF4297-STAND (Type 3) with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T2, T3, T7, PhiV-1 (Gao et al., 2020)
Subsystem Mrr-STAND (Type 4) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T3, T7, PhiV-1 (Gao et al., 2020)
Subsystem SIR2-STAND (Type 5) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2 (Gao et al., 2020)
Subsystem SeAvs1 with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against P1, ZL-19 (Gao et al., 2022)
Subsystem EcAcs1 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against ZL-19 (Gao et al., 2022)
Subsystem EpAvs1 with a system from *Erwinia piriflorinigrans* in *Escherichia coli* has an anti-phage effect against P1, Lambda, , ZL-19 (Gao et al., 2022)
Subsystem SeAvs3 with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022)
Subsystem KvAvs3 with a system from *Klebsiella variicola* in *Escherichia coli* has an anti-phage effect against P1, ZL-19 (Gao et al., 2022)
Subsystem EcAvs2 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, P1, T4, T5, ZL-19 (Gao et al., 2022)
Subsystem Ec2Avs2 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1 (Gao et al., 2022)
Subsystem EcAvs4 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022)
Subsystem Ec2Avs4 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022)
Subsystem KpAvs4 with a system from *Klebsiella pneumoniae* in *Escherichia coli* has an anti-phage effect against ZL-19 (Gao et al., 2022)
Subsystem CcAvs4 with a system from *Corallococcus coralloides* in *Escherichia coli* has an anti-phage effect against T7 (Gao et al., 2022)
## Relevant abstracts
**Gao, L. A. et al. Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science 377, eabm4096 (2022).**
Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain-like receptors (NLRs) of the STAND superfamily that are ubiquitous in plants, animals, and fungi. Although the roles of NLRs in eukaryotic immunity are well established, it is unknown whether prokaryotes use similar defense mechanisms. Here, we show that antiviral STAND (Avs) homologs in bacteria and archaea detect hallmark viral proteins, triggering Avs tetramerization and the activation of diverse N-terminal effector domains, including DNA endonucleases, to abrogate infection. Cryo-electron microscopy reveals that Avs sensor domains recognize conserved folds, active-site residues, and enzyme ligands, allowing a single Avs receptor to detect a wide variety of viruses. These findings extend the paradigm of pattern recognition of pathogen-specific proteins across all three domains of life.
**Gao, L. et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077-1084 (2020).**
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.
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# Abi2
## Example of genomic structure
The Abi2 system is composed of one protein: Abi_2.
Here is an example found in the RefSeq database:
<img src="./data/Abi2.svg">
Abi2 system in the genome of *Clostridium butyricum* (GCF\_014131795.1) is composed of 1 protein: Abi\_2 (WP\_035763709.1).
## Distribution of the system among prokaryotes
The Abi2 system is present in a total of 176 different species.
Among the 22k complete genomes of RefSeq, this system is present in 1210 genomes (5.3 %).
<img src="./data/Distribution_Abi2.svg" width=800px>
*Proportion of genome encoding the Abi2 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Relevant abstracts
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# AbiA
## Example of genomic structure
The AbiA system have been describe in a total of 2 subsystems.
Here is some example found in the RefSeq database:
<img src="./data/AbiA_large.svg">
AbiA\_large subsystem in the genome of *Lactobacillus amylovorus* (GCF\_002706375.1) is composed of 1 protein: AbiA\_large (WP\_056940268.1).
<img src="./data/AbiA_small.svg">
AbiA\_small subsystem in the genome of *Mesobacillus foraminis* (GCF\_003667765.1) is composed of 2 proteins: AbiA\_small (WP\_121614402.1)and, AbiA\_SLATT (WP\_121614403.1).
## Distribution of the system among prokaryotes
The AbiA system is present in a total of 35 different species.
Among the 22k complete genomes of RefSeq, this system is present in 50 genomes (0.2 %).
<img src="./data/Distribution_AbiA.svg" width=800px>
*Proportion of genome encoding the AbiA system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
## Experimental validation
AbiA systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
**Mestre, M. R. et al. UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions. Nucleic Acids Research 50, 6084-6101 (2022).**
Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.
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# AbiB
## Example of genomic structure
The AbiB system is composed of one protein: AbiB.
Here is an example found in the RefSeq database:
<img src="./data/AbiB.svg">
AbiB system in the genome of *Lactococcus lactis* (GCF\_020221755.1) is composed of 1 protein: AbiB (WP\_047687114.1).
## Distribution of the system among prokaryotes
The AbiB system is present in a total of 5 different species.
Among the 22k complete genomes of RefSeq, this system is present in 13 genomes (0.1 %).
<img src="./data/Distribution_AbiB.svg" width=800px>
*Proportion of genome encoding the AbiB system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiB systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
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# AbiC
## Example of genomic structure
The AbiC system is composed of one protein: AbiC.
Here is an example found in the RefSeq database:
<img src="./data/AbiC.svg">
AbiC system in the genome of *Enterococcus faecium* (GCF\_012933295.2) is composed of 1 protein: AbiC (WP\_098388098.1).
## Distribution of the system among prokaryotes
The AbiC system is present in a total of 110 different species.
Among the 22k complete genomes of RefSeq, this system is present in 196 genomes (0.9 %).
<img src="./data/Distribution_AbiC.svg" width=800px>
*Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiC systems were experimentally validated using:
A system from *Klebsiella pneumoniae's PICI (KpCIFDAARGOS_1313)* in *Escherichia coli* has an anti-phage effect against T5, Lambda, HK97, HK544, HK578, T7 (Fillol-Salom et al., 2022)
A system from *Klebsiella pneumoniae's PICI (KpCIFDAARGOS_1313)* in *Salmonella enterica* has an anti-phage effect against P22, BTP1, ES18 (Fillol-Salom et al., 2022)
A system from *Klebsiella pneumoniae's PICI (KpCIFDAARGOS_1313)* in *Klebsiella pneumoniae* has an anti-phage effect against Pokey, Raw, Eggy (Fillol-Salom et al., 2022)
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, P335 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
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# AbiD
## Example of genomic structure
The AbiD system is composed of one protein: AbiD.
Here is an example found in the RefSeq database:
<img src="./data/AbiD.svg">
AbiD system in the genome of *Lachnospira eligens* (GCF\_020735745.1) is composed of 1 protein: AbiD (WP\_041688924.1).
## Distribution of the system among prokaryotes
The AbiD system is present in a total of 874 different species.
Among the 22k complete genomes of RefSeq, this system is present in 2748 genomes (12.1 %).
<img src="./data/Distribution_AbiD.svg" width=800px>
*Proportion of genome encoding the AbiD system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiD systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
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# AbiE
## Description
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 system.
## Molecular 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.
## Example of genomic structure
The AbiE system is composed of 2 proteins: AbiEi_1 and, AbiEii.
Here is an example found in the RefSeq database:
<img src="./data/AbiE.svg">
AbiE system in the genome of *Desulfuromonas versatilis* (GCF\_019704135.1) is composed of 2 proteins: AbiEi\_1 (WP\_221251730.1)and, AbiEii (WP\_221251731.1).
## Distribution of the system among prokaryotes
The AbiE system is present in a total of 962 different species.
Among the 22k complete genomes of RefSeq, this system is present in 3742 genomes (16.4 %).
<img src="./data/Distribution_AbiE.svg" width=800px>
*Proportion of genome encoding the AbiE system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiE systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Dy, R. L., Przybilski, R., Semeijn, K., Salmond, G. P. C. & Fineran, P. C. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res 42, 4590-4605 (2014).**
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 ? 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.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
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# AbiG
## Example of genomic structure
The AbiG system is composed of 2 proteins: AbiGi and, AbiGii.
Here is an example found in the RefSeq database:
<img src="./data/AbiG.svg">
AbiG system in the genome of *Streptococcus mutans* (GCF\_009738105.1) is composed of 2 proteins: AbiGi (WP\_002266883.1)and, AbiGii (WP\_002266884.1).
## Distribution of the system among prokaryotes
The AbiG system is present in a total of 23 different species.
Among the 22k complete genomes of RefSeq, this system is present in 33 genomes (0.1 %).
<img src="./data/Distribution_AbiG.svg" width=800px>
*Proportion of genome encoding the AbiG system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiG systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
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# AbiH
## Example of genomic structure
The AbiH system is composed of one protein: AbiH.
Here is an example found in the RefSeq database:
<img src="./data/AbiH.svg">
AbiH system in the genome of *Agrobacterium tumefaciens* (GCF\_005221405.1) is composed of 1 protein: AbiH (WP\_045021548.1).
## Distribution of the system among prokaryotes
The AbiH system is present in a total of 408 different species.
Among the 22k complete genomes of RefSeq, this system is present in 1277 genomes (5.6 %).
<img src="./data/Distribution_AbiH.svg" width=800px>
*Proportion of genome encoding the AbiH system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiH systems were experimentally validated using:
A system from *lactococci* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
**Prévots, F., Daloyau, M., Bonin, O., Dumont, X. & Tolou, S. Cloning and sequencing of the novel abortive infection gene abiH of Lactococcus lactis ssp. lactis biovar. diacetylactis S94. FEMS Microbiol Lett 142, 295-299 (1996).**
A gene which encodes resistance by abortive infection (Abi+) to bacteriophage was cloned from Lactococcus lactis ssp. lactis biovar. diacetylactis S94. This gene was found to confer a reduction in efficiency of plating and plaque size for prolate-headed bacteriophage phi 53 (group I of homology) and total resistance to the small isometric-headed bacteriophage phi 59 (group III of homology). The cloned gene is predicted to encode a polypeptide of 346 amino acid residues with a deduced molecular mass of 41 455 Da. No homology with any previously described genes was found. A probe was used to determine the presence of this gene in two strains on 31 tested.
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# AbiI
## Example of genomic structure
The AbiI system is composed of one protein: AbiI.
Here is an example found in the RefSeq database:
<img src="./data/AbiI.svg">
AbiI system in the genome of *Enterococcus faecalis* (GCF\_002814115.1) is composed of 1 protein: AbiI (WP\_002367720.1).
## Distribution of the system among prokaryotes
The AbiI system is present in a total of 8 different species.
Among the 22k complete genomes of RefSeq, this system is present in 8 genomes (0.0 %).
<img src="./data/Distribution_AbiI.svg" width=800px>
*Proportion of genome encoding the AbiI system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiI systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
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# AbiJ
## Example of genomic structure
The AbiJ system is composed of one protein: AbiJ.
Here is an example found in the RefSeq database:
<img src="./data/AbiJ.svg">
AbiJ system in the genome of *Loigolactobacillus backii* (GCF\_001663735.1) is composed of 1 protein: AbiJ (WP\_068377534.1).
## Distribution of the system among prokaryotes
The AbiJ system is present in a total of 321 different species.
Among the 22k complete genomes of RefSeq, this system is present in 807 genomes (3.5 %).
<img src="./data/Distribution_AbiJ.svg" width=800px>
*Proportion of genome encoding the AbiJ system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiJ systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
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# AbiK
## Example of genomic structure
The AbiK system is composed of one protein: AbiK.
Here is an example found in the RefSeq database:
<img src="./data/AbiK.svg">
AbiK system in the genome of *Lactococcus lactis* (GCF\_002078995.2) is composed of 1 protein: AbiK (WP\_081199340.1).
## Distribution of the system among prokaryotes
The AbiK system is present in a total of 32 different species.
Among the 22k complete genomes of RefSeq, this system is present in 107 genomes (0.5 %).
<img src="./data/Distribution_AbiK.svg" width=800px>
*Proportion of genome encoding the AbiK system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiK systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
**Mestre, M. R. et al. UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions. Nucleic Acids Research 50, 6084-6101 (2022).**
Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.
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# AbiL
## Example of genomic structure
The AbiL system is composed of 2 proteins: AbiLii2 and, AbiLi2.
Here is an example found in the RefSeq database:
<img src="./data/AbiL.svg">
AbiL system in the genome of *Fusobacterium nucleatum* (GCF\_003019785.1) is composed of 2 proteins: AbiLii2 (WP\_005903821.1)and, AbiLi2 (WP\_005903823.1).
## Distribution of the system among prokaryotes
The AbiL system is present in a total of 456 different species.
Among the 22k complete genomes of RefSeq, this system is present in 783 genomes (3.4 %).
<img src="./data/Distribution_AbiL.svg" width=800px>
*Proportion of genome encoding the AbiL system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiL systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
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# AbiN
## Example of genomic structure
The AbiN system is composed of one protein: AbiN.
Here is an example found in the RefSeq database:
<img src="./data/AbiN.svg">
AbiN system in the genome of *Enterococcus faecalis* (GCF\_016743895.1) is composed of 1 protein: AbiN (WP\_002384355.1).
## Distribution of the system among prokaryotes
The AbiN system is present in a total of 51 different species.
Among the 22k complete genomes of RefSeq, this system is present in 167 genomes (0.7 %).
<img src="./data/Distribution_AbiN.svg" width=800px>
*Proportion of genome encoding the AbiN system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiN systems were experimentally validated using:
A system from *lactococcal prophage* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
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# AbiO
## Example of genomic structure
The AbiO system is composed of one protein: AbiO.
Here is an example found in the RefSeq database:
<img src="./data/AbiO.svg">
AbiO system in the genome of *Pasteurella multocida* (GCF\_016313205.1) is composed of 1 protein: AbiO (WP\_005752771.1).
## Distribution of the system among prokaryotes
The AbiO system is present in a total of 67 different species.
Among the 22k complete genomes of RefSeq, this system is present in 109 genomes (0.5 %).
<img src="./data/Distribution_AbiO.svg" width=800px>
*Proportion of genome encoding the AbiO system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiO systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
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# AbiP2
## Example of genomic structure
The AbiP2 system is composed of one protein: AbiP2.
Here is an example found in the RefSeq database:
<img src="./data/AbiP2.svg">
AbiP2 system in the genome of *Casimicrobium huifangae* (GCF\_009746125.1) is composed of 1 protein: AbiP2 (WP\_156862066.1).
## Distribution of the system among prokaryotes
The AbiP2 system is present in a total of 98 different species.
Among the 22k complete genomes of RefSeq, this system is present in 299 genomes (1.3 %).
<img src="./data/Distribution_AbiP2.svg" width=800px>
*Proportion of genome encoding the AbiP2 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiP2 systems were experimentally validated using:
Subsystem RT-Abi-P2 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Gao et al., 2020)
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
**Mestre, M. R. et al. UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions. Nucleic Acids Research 50, 6084-6101 (2022).**
Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.
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# AbiQ
## Example of genomic structure
The AbiQ system is composed of one protein: AbiQ.
Here is an example found in the RefSeq database:
<img src="./data/AbiQ.svg">
AbiQ system in the genome of *Enterococcus sp.* (GCF\_003812305.1) is composed of 1 protein: AbiQ (WP\_123866849.1).
## Distribution of the system among prokaryotes
The AbiQ system is present in a total of 110 different species.
Among the 22k complete genomes of RefSeq, this system is present in 262 genomes (1.1 %).
<img src="./data/Distribution_AbiQ.svg" width=800px>
*Proportion of genome encoding the AbiQ system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiQ systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Emond, E. et al. AbiQ, an abortive infection mechanism from Lactococcus lactis. Appl Environ Microbiol 64, 4748-4756 (1998).**
Lactococcus lactis W-37 is highly resistant to phage infection. The cryptic plasmids from this strain were coelectroporated, along with the shuttle vector pSA3, into the plasmid-free host L. lactis LM0230. In addition to pSA3, erythromycin- and phage-resistant isolates carried pSRQ900, an 11-kb plasmid from L. lactis W-37. This plasmid made the host bacteria highly resistant (efficiency of plaquing <10(-8)) to c2- and 936-like phages. pSRQ900 did not confer any resistance to phages of the P335 species. Adsorption, cell survival, and endonucleolytic activity assays showed that pSRQ900 encodes an abortive infection mechanism. The phage resistance mechanism is limited to a 2.2-kb EcoRV/BclI fragment. Sequence analysis of this fragment revealed a complete open reading frame (abiQ), which encodes a putative protein of 183 amino acids. A frameshift mutation within abiQ completely abolished the resistant phenotype. The predicted peptide has a high content of positively charged residues (pI = 10.5) and is, in all likelihood, a cytosolic protein. AbiQ has no homology to known or deduced proteins in the databases. DNA replication assays showed that phage c21 (c2-like) and phage p2 (936-like) can still replicate in cells harboring AbiQ. However, phage DNA accumulated in its concatenated form in the infected AbiQ+ cells, whereas the AbiQ- cells contained processed (mature) phage DNA in addition to the concatenated form. The production of the major capsid protein of phage c21 was not hindered in the cells harboring AbiQ.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
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# AbiR
## Example of genomic structure
The AbiR system is composed of 3 proteins: AbiRc, AbiRb and, AbiRa.
Here is an example found in the RefSeq database:
<img src="./data/AbiR.svg">
AbiR system in the genome of *Pediococcus pentosaceus* (GCF\_019614475.1) is composed of 3 proteins: AbiRa (WP\_220689027.1), AbiRb (WP\_011673124.1)and, AbiRc (WP\_011673125.1).
## Distribution of the system among prokaryotes
The AbiR system is present in a total of 31 different species.
Among the 22k complete genomes of RefSeq, this system is present in 56 genomes (0.2 %).
<img src="./data/Distribution_AbiR.svg" width=800px>
*Proportion of genome encoding the AbiR system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiR systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against c2 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
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# AbiT
## Example of genomic structure
The AbiT system is composed of 2 proteins: AbiTii and, AbiTi.
Here is an example found in the RefSeq database:
<img src="./data/AbiT.svg">
AbiT system in the genome of *Sphaerochaeta associata* (GCF\_022869165.1) is composed of 2 proteins: AbiTi (WP\_244771454.1)and, AbiTii (WP\_244771455.1).
## Distribution of the system among prokaryotes
The AbiT system is present in a total of 5 different species.
Among the 22k complete genomes of RefSeq, this system is present in 8 genomes (0.0 %).
<img src="./data/Distribution_AbiT.svg" width=800px>
*Proportion of genome encoding the AbiT system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiT systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, P335 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
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# AbiU
## Example of genomic structure
The AbiU system is composed of one protein: AbiU.
Here is an example found in the RefSeq database:
<img src="./data/AbiU.svg">
AbiU system in the genome of *Fulvivirga lutea* (GCF\_017068455.1) is composed of 1 protein: AbiU (WP\_205721428.1).
## Distribution of the system among prokaryotes
The AbiU system is present in a total of 390 different species.
Among the 22k complete genomes of RefSeq, this system is present in 1017 genomes (4.5 %).
<img src="./data/Distribution_AbiU.svg" width=800px>
*Proportion of genome encoding the AbiU system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Experimental validation
AbiU systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
## Relevant abstracts
**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
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