Avs
Contributors: Alex Linyi Gao, Nathalie Bechon
Avs proteins are members of the STAND (signal transduction ATPase with numerous domains) superfamily of P-loop NTPases, which play essential roles in innate immunity and programmed cell death in eukaryotes (N/A, N/A) . STAND ATPases include nucleotide-binding oligomerization domain-like receptors (NLRs) in animal inflammasomes and plant resistosomes. Bacterial Avs share a common tripartite domain architecture with eukaryotic NLR, typically consisting of a central ATPase, a C-terminal sensor with superstructure-forming repeats, and an N-terminal effector involved in inflammation or cell death. They are very similar to other bacterial defense systems: bNACHT, CARD_NLR , Rst_TIR-NLR.
Info
Two classifications of Avs systems were proposed. The first one (N/A) distinguishes 5 types of Avs based on their effector domain. This is the classification used in Defense Finder right now, and in the following wiki entry unless stated otherwise. Considering the modular aspect of the effector domain, a new classification based on the homology of the NTPase and C terminal sensor domain, and not on the effector domain, has been proposed more recently (N/A) and is the one used in this description of the mechanism. This second classification defines 4 different types, that do not represent the whole diversity of Avs proteins but only the 4 characterized types.
Similar to their eukaryotic counterparts, Avs proteins utilize their C-terminal sensor domains to bind to pathogen-associated molecular patterns (PAMPs). Specifically, Avs1, Avs2, and Avs3 bind to monomers of the large terminase subunit of tailed phages, which account for approximately 96% of all phages, whereas Avs4 binds to monomers of the portal protein. The helical sensor domains of Avs1-4 can recognize diverse variants of terminase or portal proteins, with less than 5% sequence identity in some cases. Binding is mediated by shape complementarity across an extended interface, indicating fold recognition. Additionally, Avs3 directly recognizes active site residues and the ATP ligand of the large terminase.
Upon binding to their cognate phage protein, Avs1-4 assemble into tetramers that activate their N-terminal effector domains, which are often non-specific dsDNA endonucleases. The effector domains are thought to induce abortive infection to disrupt the production of progeny phage.
Avs systems sometimes include additional essential small genes on top of the canonical Avs gene, but the way they contribute to defense is not currently described.
The Avs system has been described in a total of 5 subsystems (in the old classification).
Here are some examples found in the RefSeq database:
The Avs_I system in Priestia aryabhattai (GCF_022811825.1, NZ_CP064098) is composed of 3 proteins Avs1C (WP_243495694.1) Avs1B (WP_243495695.1) Avs1A (WP_243495696.1)
The Avs_II system in Haloferax volcanii (GCF_000025685.1, NC_013967) is composed of 1 protein: Avs2A (WP_013035348.1)
The Avs_III system in Chryseobacterium indologenes (GCF_002208925.2, NZ_CP022058) is composed of 2 proteins Avs3B (WP_002978689.1) Avs3A (WP_088583894.1)
The Avs_IV system in Dysosmobacter welbionis (GCF_005121165.3, NZ_CP034413) is composed of 1 protein: Avs4A (WP_136890703.1)
The Avs_V system in Klebsiella variicola (GCF_015287155.1, NZ_CP063912) is composed of 1 protein: Avs5A (WP_131026359.1)
Among the NaN complete genomes of RefSeq, the Avs is detected in NaN genomes (NaN %). The system was detected in NaN different species.
Percent genome having the system
Minimum genomes count to display
graph LR;
Fillol-Salom_2022[Fillol-Salom et al., 2022] --> Origin_0
Origin_0[ SIR2-STAND
Escherichia fergusonii's PICI EfCIRHB19-C05
QML19490.1] --> Expressed_0[Escherichia coli]
Expressed_0[Escherichia coli] ----> T4 & Lambda & HK97 & HK544 & HK578 & T7
Fillol-Salom_2022[Fillol-Salom et al., 2022] --> Origin_0
Origin_0[ SIR2-STAND
Escherichia fergusonii's PICI EfCIRHB19-C05
QML19490.1] --> Expressed_1[Salmonella enterica]
Expressed_1 ----> P22 & BTP1 & ES18 & det7
Fillol-Salom_2022[Fillol-Salom et al., 2022] --> Origin_0
Origin_0[ SIR2-STAND
Escherichia fergusonii's PICI EfCIRHB19-C05
QML19490.1] --> Expressed_2[Klebsiella pneumoniae]
Expressed_2[Klebsiella pneumoniae] ----> Pokey
Gao_2020[Gao et al., 2020] --> Origin_1
Origin_1[ Metallo beta-lactamase + protease + STAND type 1
Erwinia piriflorinigrans
WP_023654314.1, WP_084007836.1,
WP_023654316.1] --> Expressed_3[Escherichia coli]
Expressed_3[Escherichia coli] ----> P1
Gao_2020[Gao et al., 2020] --> Origin_2
Origin_2[ STAND type 2
Escherichia coli
WP_063118745.1] --> Expressed_4[Escherichia coli]
Expressed_4[Escherichia coli] ----> T4 & P1
Gao_2022[Gao et al., 2022] --> Origin_2
Origin_2[ EcAvs2
Escherichia coli
WP_063118745.1] --> Expressed_4[Escherichia coli]
Expressed_4[Escherichia coli] ----> T7 & PhiV-1 & P1 & T4 & T5 & ZL-19
Gao_2020[Gao et al., 2020] --> Origin_3
Origin_3[ DUF4297-STAND type 3
Salmonella enterica
WP_126523998.1, WP_126523997.1] --> Expressed_5[Escherichia coli]
Expressed_5[Escherichia coli] ----> T2 & T3 & T7 & PhiV-1
Gao_2020[Gao et al., 2020] --> Origin_4
Origin_4[ Mrr-STAND type 4
Escherichia coli
WP_044068927.1] --> Expressed_6[Escherichia coli]
Expressed_6[Escherichia coli] ----> T3 & T7 & PhiV-1
Gao_2022[Gao et al., 2022] --> Origin_4
Origin_4[ EcAvs4
Escherichia coli
WP_044068927.1] --> Expressed_6[Escherichia coli]
Expressed_6[Escherichia coli] ----> T7 & PhiV-1 & ZL-19
Gao_2020[Gao et al., 2020] --> Origin_5
Origin_5[ SIR2-STAND type 5
Escherichia coli
WP_001515187.1] --> Expressed_7[Escherichia coli]
Expressed_7[Escherichia coli] ----> T2
Gao_2022[Gao et al., 2022] --> Origin_6
Origin_6[ SeAvs1
Salmonella enterica
ECC9552481.1] --> Expressed_8[Escherichia coli]
Expressed_8[Escherichia coli] ----> P1 & ZL-19
Gao_2022[Gao et al., 2022] --> Origin_7
Origin_7[ EcAvs1
Escherichia coli
WP_060615938.1] --> Expressed_9[Escherichia coli]
Expressed_9[Escherichia coli] ----> ZL-19
Gao_2022[Gao et al., 2022] --> Origin_8
Origin_8[ EpAvs1
Erwinia piriflorinigrans
WP_048696970.1] --> Expressed_10[Escherichia coli]
Expressed_10[Escherichia coli] ----> P1 & Lambda & ZL-19
Gao_2022[Gao et al., 2022] --> Origin_9
Origin_9[ SeAvs3
Salmonella enterica
WP_126523998.1] --> Expressed_11[Escherichia coli]
Expressed_11[Escherichia coli] ----> T7 & PhiV-1 & ZL-19
Gao_2022[Gao et al., 2022] --> Origin_10
Origin_10[ KvAvs3
Klebsiella variicola
WP_139964370.1] --> Expressed_12[Escherichia coli]
Expressed_12[Escherichia coli] ----> P1 & ZL-19
Gao_2022[Gao et al., 2022] --> Origin_11
Origin_11[ Ec2Avs2
Escherichia coli
WP_001017806.1] --> Expressed_13[Escherichia coli]
Expressed_13[Escherichia coli] ----> P1
Gao_2022[Gao et al., 2022] --> Origin_12
Origin_12[ Ec2Avs4
Escherichia coli
EEW5978513.1] --> Expressed_14[Escherichia coli]
Expressed_14[Escherichia coli] ----> T7 & PhiV-1 & ZL-19
Gao_2022[Gao et al., 2022] --> Origin_13
Origin_13[ KpAvs4
Klebsiella pneumoniae
WP_087775949.1] --> Expressed_15[Escherichia coli]
Expressed_15[Escherichia coli] ----> ZL-19
Gao_2022[Gao et al., 2022] --> Origin_14
Origin_14[ CcAvs4
Corallococcus coralloides
WP_083892326.1] --> Expressed_16[Escherichia coli]
Expressed_16[Escherichia coli] ----> T7
subgraph Title1[Reference]
Fillol-Salom_2022
Gao_2020
Gao_2022
end
subgraph Title2[System origin]
Origin_0
Origin_0
Origin_0
Origin_1
Origin_2
Origin_2
Origin_3
Origin_4
Origin_4
Origin_5
Origin_6
Origin_7
Origin_8
Origin_9
Origin_10
Origin_11
Origin_12
Origin_13
Origin_14
end
subgraph Title3[Expression species]
Expressed_0
Expressed_1
Expressed_2
Expressed_3
Expressed_4
Expressed_4
Expressed_5
Expressed_6
Expressed_6
Expressed_7
Expressed_8
Expressed_9
Expressed_10
Expressed_11
Expressed_12
Expressed_13
Expressed_14
Expressed_15
Expressed_16
end
subgraph Title4[Protects against]
T4
Lambda
HK97
HK544
HK578
T7
P22
BTP1
ES18
det7
Pokey
P1
T4
P1
T7
PhiV-1
P1
T4
T5
ZL-19
T2
T3
T7
PhiV-1
T3
T7
PhiV-1
T7
PhiV-1
ZL-19
T2
P1
ZL-19
ZL-19
P1
Lambda
ZL-19
T7
PhiV-1
ZL-19
P1
ZL-19
P1
T7
PhiV-1
ZL-19
ZL-19
T7
end
style Title1 fill:none,stroke:none,stroke-width:none
style Title2 fill:none,stroke:none,stroke-width:none
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none