nlr.md

title: NLR
layout: article
tableColumns:
    article:
      doi: 10.1101/2022.07.19.500537
      abstract: |
        Bacteria use a wide range of immune systems to counter phage infection. A subset of these genes share homology with components of eukaryotic immune systems, suggesting that eukaryotes horizontally acquired certain innate immune genes from bacteria. Here we show that proteins containing a NACHT module, the central feature of the animal nucleotide-binding domain and leucine-rich repeat containing gene family (NLRs), are found in bacteria and defend against phages. NACHT proteins are widespread in bacteria, provide immunity against both DNA and RNA phages, and display the characteristic C-terminal sensor, central NACHT, and N-terminal effector modules. Some bacterial NACHT proteins have domain architectures similar to human NLRs that are critical components of inflammasomes. Human disease-associated NLR mutations that cause stimulus-independent activation of the inflammasome also activate bacterial NACHT proteins, supporting a shared signaling mechanism. This work establishes that NACHT module-containing proteins are ancient mediators of innate immunity across the tree of life.
    Sensor: Unknown
    Activator: Unknown
    Effector: Unknown
    PFAM: PF05729

NLR

Example of genomic structure

A total of 2 subsystems have been described for the NLR system.

Here is some examples found in the RefSeq database:

The NLR_like_bNACHT01 system in Colwellia sp. Arc7-D (GCF_003061515.1, NZ_CP028924) is composed of 1 protein: NLR_like_bNACHT01 (WP_162533747.1)

The NLR_like_bNACHT09 system in Parabacteroides johnsonii (GCF_020735865.1, NZ_CP085975) is composed of 1 protein: NLR_like_bNACHT09 (WP_009859882.1)

Distribution of the system among prokaryotes

Among the 22,803 complete genomes of RefSeq, the NLR is detected in 453 genomes (1.99 %).

The system was detected in 205 different species.

Proportion of genome encoding the NLR system for the 14 phyla with more than 50 genomes in the RefSeq database.

Structure

NLR_like_bNACHT01

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height: 700 dataUrl: /nlr/NLR_like_bNACHT01__NLR_like_bNACHT01-plddts_87.90581.pdb

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NLR_like_bNACHT09

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height: 700 dataUrl: /nlr/NLR_like_bNACHT09__NLR_like_bNACHT09-plddts_85.63627.pdb

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Experimental validation

graph LR; Kibby_2022[Kibby et al., 2022] --> Origin_0 Origin_0[ bNACHT01 Klebsiella pneumoniae WP_015632533.1] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T4 & T5 & T6 Kibby_2022[Kibby et al., 2022] --> Origin_1 Origin_1[ bNACHT02 Escherichia coli WP_021557529.1] --> Expressed_1[Escherichia coli] Expressed_1[Escherichia coli] ----> T7 & MS2 Kibby_2022[Kibby et al., 2022] --> Origin_2 Origin_2[ bNACHT11 Klebsiella pneumoniae WP_114260439.1] --> Expressed_2[Escherichia coli] Expressed_2[Escherichia coli] ----> T2 & T4 & T6 Kibby_2022[Kibby et al., 2022] --> Origin_3 Origin_3[ bNACHT12 Escherichia coli WP_021519735.1] --> Expressed_3[Escherichia coli] Expressed_3[Escherichia coli] ----> T4 & T6 & MS2 Kibby_2022[Kibby et al., 2022] --> Origin_4 Origin_4[ bNACHT23 Escherichia coli WP_000433597.1] --> Expressed_4[Escherichia coli] Expressed_4[Escherichia coli] ----> T2 & T6 & T5 Kibby_2022[Kibby et al., 2022] --> Origin_5 Origin_5[ bNACHT25 Escherichia coli WP_001702659.1] --> Expressed_5[Escherichia coli] Expressed_5[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & MS2 Kibby_2022[Kibby et al., 2022] --> Origin_6 Origin_6[ bNACHT32 Escherichia coli WP_057688292] --> Expressed_6[Escherichia coli] Expressed_6[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & MS2 Kibby_2022[Kibby et al., 2022] --> Origin_7 Origin_7[ bNACHT67 Klebsiella michiganensis WP_064381242] --> Expressed_7[Escherichia coli] Expressed_7[Escherichia coli] ----> T2 & T4 Kibby_2022[Kibby et al., 2022] --> Origin_8 Origin_8[ bNACHT09 Escherichia coli WP_087866631] --> Expressed_8[Escherichia coli] Expressed_8[Escherichia coli] ----> T2 & T4 & T5 & LambdaVir & T3 & T7 subgraph Title1[Reference] Kibby_2022 end subgraph Title2[System origin] Origin_0 Origin_1 Origin_2 Origin_3 Origin_4 Origin_5 Origin_6 Origin_7 Origin_8 end subgraph Title3[Expression species] Expressed_0 Expressed_1 Expressed_2 Expressed_3 Expressed_4 Expressed_5 Expressed_6 Expressed_7 Expressed_8 end subgraph Title4[Phage infected] T4 T5 T6 T7 MS2 T2 T4 T6 T4 T6 MS2 T2 T6 T5 T2 T4 T6 LambdaVir MS2 T2 T4 T6 LambdaVir MS2 T2 T4 T2 T4 T5 LambdaVir T3 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 ## Relevant abstracts

::relevant-abstracts

items: - doi: 10.1101/2022.07.19.500537

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