Lamassu-Fam

Contributors: Matthieu Haudiquet, Aude Bernheim

Description

The original types of Lamassu systems are Lamassu Type 1 () and Type 2 () . They both necessarily comprise two genes lmuA and lmuB, to which a third gene (lmuC) is added in the case of Lamassu Type 2.  

Lamassu has been suggested to be a large family of defense systems, that can be classified into multiple subtypes ()

These systems all encode the lmuB gene, and in most cases also comprise lmuC. In addition to these two core genes, Lamassu systems of various subtypes encode a third protein, hypothesized to be the Abi effector protein () . This effector  can be proteins encoding endonuclease domains, SIR2-domains, or even hydrolase domains () . Systems of the extended Lamassu family can be found in 10% of prokaryotic genomes () .

Lamassu were also described as DdmABC in Vibrio cholerae (, ) . They were found to be anti plasmids and thus to eliminate plasmids from the seventh pandemic Vibrio cholerae* () . The DdmABC system corresponds to a Lamassu-Fam Cap4 nuclease system.

Molecular mechanism

Lamassu systems function through abortive infection (Abi), but the molecular mechanism remains to be described. It was shown that, in Vibrio cholerae palindromic DNA sequences that are predicted to form stem-loop hairpin trigger the system () .

Example of genomic structure

The majority of the Lamassu-Fam systems are composed of 3 proteins: LmuA, LmuB and, an accessory LmuC proteins. LmuA is the effector and encode for different domains depending on the subsystem.

A total of 11 subsystems have been described for the Lamassu-Fam system.

Here are some examples found in the RefSeq database:

The Lamassu-Amidase system in Variovorax sp. PBL-H6 (GCF_901827155.1, NZ_LR594659) is composed of 2 proteins LmuA_effector_Amidase (WP_162575880.1) LmuB_SMC_Amidase (WP_162575881.1)

The Lamassu-Cap4_nuclease system in Opitutus terrae (GCF_000019965.1, NC_010571) is composed of 3 proteins LmuA_effector_Cap4_nuclease_II (WP_012377261.1) LmuC_acc_Lipase (WP_012377262.1) LmuB_SMC_Lipase (WP_012377263.1)

The Lamassu-FMO system in Mesorhizobium sp. B2-1-8 (GCF_006442545.2, NZ_CP083952) is composed of 3 proteins LmuA_effector_FMO (WP_181178269.1) LmuC_acc_FMO (WP_140755520.1) LmuB_SMC_FMO (WP_181178271.1)

The Lamassu-Hydrolase_Protease system in Deefgea piscis (GCF_013284055.1, NZ_CP054143) is composed of 4 proteins LmuA_effector_Hydrolase (WP_173533336.1) LmuA_effector_Protease (WP_173533337.1) LmuC_acc_hydrolase_protease (WP_173533338.1) LmuB_SMC_Hydrolase_protease (WP_173533339.1)

The Lamassu-Hypothetical system in Dehalococcoides mccartyi (GCF_002007905.1, NZ_CP019866) is composed of 3 proteins LmuA_effector_hypothetical (WP_077975422.1) LmuC_acc_hypothetical (WP_077975423.1) LmuB_SMC_hypothetical (WP_077975424.1)

The Lamassu-Lipase system in Klebsiella michiganensis (GCF_022869885.1, NZ_CP094999) is composed of 3 proteins LmuB_SMC_Lipase (WP_016157240.1) LmuC_acc_Lipase (WP_032931759.1) LmuA_effector_Lipase (WP_042945865.1)

The Lamassu-Mrr system in Agrobacterium tumefaciens (GCF_022760295.1, NZ_CP092895) is composed of 3 proteins LmuA_effector_Mrr (WP_223215665.1) LmuC_acc_Mrr (WP_220318798.1) LmuB_SMC_Mrr (WP_220318797.1)

The Lamassu-PDDEXK system in Corynebacterium pseudodiphtheriticum (GCF_023509295.1, NZ_CP091864) is composed of 3 proteins LmuC_acc_PDDEXK (WP_249620350.1) LmuB_SMC_PDDEXK (WP_249620351.1) LmuA_effector_PDDEXK (WP_249620352.1)

The Lamassu-Protease system in Enterococcus hirae (GCF_014218175.1, NZ_CP042289) is composed of 3 proteins LmuA_effector_Protease (WP_034866244.1) LmuC_acc_hydrolase_protease (WP_181916367.1) LmuB_SMC_Hydrolase_protease (WP_034866249.1)

The Lamassu-Sir2 system in Enterococcus faecalis (GCF_023375525.1, NZ_CP091235) is composed of 3 proteins LmuA_effector_Sir2 (WP_231436660.1) LmuC_acc_Sir2 (WP_231436659.1) LmuB_SMC_Sir2 (WP_231436658.1)

Distribution of the system among prokaryotes

Among the 22,803 complete genomes of RefSeq, the Lamassu-Fam is detected in 2867 genomes (12.57 %).

The system was detected in 1220 different species.

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

Structure

Lamassu-Amidase

Example 1

Lamassu-Cap4_nuclease

Example 1
Example 2

Lamassu-FMO

Example 1

Lamassu-Fam_Hydrolase_Protease

Example 1

Lamassu-Fam_Mrr

Example 1

Lamassu-Fam_PDDEXK

Example 1

Lamassu-Hypothetical

Example 1

Lamassu-Lipase

Example 1

Lamassu-Sir2

Example 1

Experimental validation

      
graph LR;
    Doron_2018[Doron et al., 2018] --> Origin_0
    Origin_0[Bacillus sp. NIO-1130 
SCC38433.1, SCC38445.1] --> Expressed_0[Bacillus subtilis]
    Expressed_0[Bacillus subtilis] ----> phi3T & SpBeta & SPR
    Doron_2018[Doron et al., 2018] --> Origin_1
    Origin_1[Bacillus cereus 
EJR12435.1, EJR12434.1] --> Expressed_1[Bacillus subtilis]
    Expressed_1[Bacillus subtilis] ----> SpBeta
    Millman_2022[Millman et al., 2022] --> Origin_2
    Origin_2[ LmuB+LmuC+Hydrolase Protease
Bacillus cereus 
2624999254, 2624999255,
2624999257, 2624999256] --> Expressed_2[Escherichia coli]
    Expressed_2[Escherichia coli] ----> T4
    Millman_2022[Millman et al., 2022] --> Origin_2
    Origin_2[ LmuB+LmuC+Hydrolase Protease
Bacillus cereus 
2624999254, 2624999255,
2624999257, 2624999256] --> Expressed_3[Bacillus subtilis]
    Expressed_3[Bacillus subtilis] ----> SpBeta & phi105 & Rho14 & SPP1 & phi29
    Millman_2022[Millman et al., 2022] --> Origin_3
    Origin_3[ LmuB+LmuC+Mrr endonuclease
Escherichia coli 
646870492, 646870494,
646870493] --> Expressed_4[Escherichia coli]
    Expressed_4[Escherichia coli] ----> LambdaVir & SECphi27
    Millman_2022[Millman et al., 2022] --> Origin_4
    Origin_4[ LmuB+LmuC+PDDEXK nuclease
Bacillus cereus 
2729045962, 2729045961,
2729045960] --> Expressed_5[Escherichia coli]
    Expressed_5[Escherichia coli] ----> LambdaVir
    Millman_2022[Millman et al., 2022] --> Origin_5
    Origin_5[ LmuB+LmuC+PDDEXK nuclease
Bacillus sp. UNCCL81 
2595091739, 2595091740,
2595091741] --> Expressed_6[Escherichia coli]
    Expressed_6[Escherichia coli] ----> LambdaVir
    Payne_2021[Payne et al., 2021] --> Origin_6
    Origin_6[ LmuA+LmuC+LmuB 
Janthinobacterium agaricidamnosum 
WP_038488270.1, WP_038488273.1,
WP_156484105.1] --> Expressed_7[Escherichia coli]
    Expressed_7[Escherichia coli] ----> T1 & T3 & T7 & LambdaVir & PVP-SE1
    Jaskolska_2022[Jaskólska et al., 2022] --> Origin_7
    Origin_7[ DdmABC
Vibrio cholerae 
WP_000466016.1, WP_000917213.1,
WP_000654528.1] --> Expressed_8[Escherichia coli]
    Expressed_8[Escherichia coli] ----> P1 & Lambda
    subgraph Title1[Reference]
        Doron_2018
        Millman_2022
        Payne_2021
        Jaskolska_2022
end
    subgraph Title2[System origin]
        Origin_0
        Origin_1
        Origin_2
        Origin_2
        Origin_3
        Origin_4
        Origin_5
        Origin_6
        Origin_7
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[Protects against]
        phi3T
        SpBeta
        SPR
        SpBeta
        T4
        SpBeta
        phi105
        Rho14
        SPP1
        phi29
        LambdaVir
        SECphi27
        LambdaVir
        LambdaVir
        T1
        T3
        T7
        LambdaVir
        PVP-SE1
        P1
        Lambda
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

    

References

10.1126/science.aar4120
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10.1016/j.chom.2022.09.017
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10.1093/nar/gkab883
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10.1038/s41586-022-04546-y
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10.1101/2022.11.18.517080
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10.1101/2022.05.11.491447
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