Agrobacterium tumefaciens deploys a superfamily of type VI secretion DNase effectors as weapons for interbacterial competition in planta

Abstract

The type VI secretion system (T6SS) is a widespread molecular weapon deployed by many Proteobacteria to target effectors/toxins into both eukaryotic and prokaryotic cells. We report that Agrobacterium tumefaciens, a soil bacterium that triggers tumorigenesis in plants, produces a family of type VI DNase effectors (Tde) that are distinct from previously known polymorphic toxins and nucleases. Tde exhibits an antibacterial DNase activity that relies on a conserved HxxD motif and can be counteracted by a cognate immunity protein, Tdi. In vitro, A. tumefaciens T6SS could kill Escherichia coli but triggered a lethal counterattack by Pseudomonas aeruginosa upon injection of the Tde toxins. However, in an in planta coinfection assay, A. tumefaciens used Tde effectors to attack both siblings cells and P. aeruginosa to ultimately gain a competitive advantage. Such acquired T6SS-dependent fitness in vivo and conservation of Tde-Tdi couples in bacteria highlights a widespread antibacterial weapon beneficial for niche colonization.

Graphical abstract

Figure 1

Atu4350 Is an A. tumefaciens T6SS-Dependent Effector (A) A. tumefaciens T6SS consists of the major T6SS gene cluster containing two operons, imp (in gray; atu4343 to atu4330) and hcp (in black; atu4344 to atu4352), and another divergent operon named vgrG2 (in white; atu3642 to atu3638) (Lin et al., 2013). The genes are indicated with locus/common names and/or designated as tss (type VI secretion) or tag (type VI secretion-associated gene) based on the proposed nomenclature (Shalom et al., 2007). The three toxins and their cognate immunity proteins identified in this study are indicated in red and green, respectively. The genes, which are essential, nonessential, or partially required for Hcp secretion, are flagged as (+), (−) or (−/+), respectively. (B) Secretion of Atu4350 is T6SS dependent. Total and secreted proteins were isolated from wild-type C58, ΔtssL mutant, and the complemented strain ΔtssL(pTssL) grown on AB-MES minimal agar (pH 5.5) for 24 hr at 25°C for western blot analysis of nonsecreted protein ActC (Liu et al., 2008), Hcp, and Atu4347, known T6SS-dependent secreted proteins. Asterisk ^∗ indicates the cross-reacting band of the antibody against Atu4347.

Figure 2

A Superfamily of Type VI DNase Effectors (A) Partial sequence alignment of the representative Tde superfamily proteins that contain the toxin_43 domain showing the conserved HxxD catalytic motif. The locus tag and organism name are on the left, and the amino acid position of residues in the alignment is indicated on each side of the sequences. The conserved amino acid residues are shaded in black for identity and in gray for similarity. Asterisks (^∗) indicate amino acids in the HxxD catalytic motif, which were targeted for mutagenesis. (B) In vitro DNase activity assay. The integrity of plasmid DNA (pTrc200) coincubated with purified proteins of the wild-type 4350 (WT) or the H190A D193A catalytic site mutant in the presence (+) or absence (−) of Mg²⁺ at 37°C for 1 hr was visualized with 1% agarose gel. Plasmid DNA with buffer (−) was a control. (C) Detection of DNA fragmentation by TUNEL assay and analysis by cell sorting. E. coli cells containing pJN105 (vector) or derivatives expressing the wild-type Atu4350 or H190A D193A catalytic site mutant were induced by L-arabinose. Cells were fixed and stained with FITC-dUTP to detect the fragmented DNA by monitoring fluorescence intensity (indicated on the x axis) by cell sorting. FITC-labeled cells are indicated as positive, and cells with background FITC signal are indicated as negative. The counts for cell sorting are indicated on the y axis. Similar results were obtained from at least two independent experiments. See also Figures S1 and S2.

Figure 3

Three Toxin-Immunity Pair Analysis (A and B) Cultures of A. tumefaciens wild-type C58 harboring the vectors (pTrc200 and pRL662) or derivatives were supplemented with 1 mM IPTG (at time 0 hr) for growth curve analysis. Atu4350 was produced from plasmid pTrc200, and the putative immunity protein Atu4351 or Atu4349 was constitutively expressed from plasmid pRL662 (A). Atu3640 was produced from plasmid pTrc200, and the putative immunity protein Atu3639 was constitutively expressed from plasmid pRL662 (B). (C) E. coli DH10B cultures were induced at 0 hr with 1 mM IPTG for 1 hr to produce the putative immunity protein Atu4346 from plasmid pTrc200, then L-arabinose (Ara) induction of Atu4347 with or without signal peptide (ssPelB) from plasmid pJN105. Cell growth was monitored by measuring OD₆₀₀ at 1 hr intervals. The growth of control cells carrying empty vectors was monitored in parallel. Data are mean ±SE of three (A) or two ([B] and [C]) independent experiments.

Figure 4

A. tumefaciens Intraspecies Competition In Planta The A. tumefaciens attacker strain was mixed with the target strain harboring plasmids pRL662 or pTrc200 at 10:1 (attacker: target) ratio and infiltrated into N. benthamiana leaves. The survival of target cells was quantified by counting CFUs on antibiotics-containing LB agar. (A) Attackers are wild-type C58, ΔtssL, or Δ3TIs (Δtae-tai, Δtde1-tdi1, Δtde2-tdi2) coinfected with target strains C58 or Δ3TIs. (B) Attacker wild-type C58 was tested against target mutants lacking single (Δtae-tai, Δ4349-tde1-tdi1, or Δtde2-tdi2) or triple toxin-immunity pairs (Δ3TIs). (C) The attacker strain C58 was coinfected with the target strains (Δ4349-tde1-tdi1 or Δtde2-tdi2) harboring plasmid pTrc200 (Vector) or derivatives expressing the cognate immunity gene. (D) Attacker strains containing vector pTrc200 (Vec) or derivatives expressing wild-type (WT) or catalytic site mutants of Tde1 (H190A D193A, H190A, or D193A) were tested against the target mutant strain Δ4349-tde1-tdi1 harboring pRL662 plasmid. Data are mean ±SE ([B]: n = 3; [A], [C], and [D]: n = 4). Significant difference compared with C58 or Vec was denoted as ^∗∗∗ = p < 0.0005, ^∗∗ = p < 0.005, and ^∗ = p < 0.05. See also Figures S4 and S5.

Figure 5

A. tumefaciens-P. aeruginosa Competition Assays (A and B) P. aeruginosa and A. tumefaciens cells were mixed equally and cocultured on LB agar ([A] and [B]) or coinfected in planta (C). (A) P. aeruginosa wild-type PAK, PAKΔretS (ΔretS), or PAKΔretSΔH1 (ΔretSΔH1) was cocultured with A. tumefaciens wild-type C58 or T6SS mutant (ΔT6SS). (B) P. aeruginosa PAK was mixed with one of the A. tumefaciens strains C58, ΔT6SS, Δ3TIs, Δtde1-tdi1Δtde2-tdi2, or Δtae-tai mutant. (C) Cells of P. aeruginosa and A. tumefaciens harboring pRL662 derivative were mixed equally and infiltrated into N. benthamiana leaves. P. aeruginosa cell number was scored after 16 hr incubation at 37°C on LB agar without any antibiotics. Data are mean ±SE ([A]: n = 4–6; [B] and [C]: n = 3–4). Significant difference compared with C58 was denoted as ^∗∗ = p < 0.005 and ^∗ = p < 0.05. See also Figures S4 and S5.

Figure 6

Illustration of A. tumefaciens Interbacterial Competition during In Planta Colonization A. tumefaciens wild-type C58 (WT, green) injects Tde toxin (red or green circle) via the T6SS puncturing device drawn between the cells. (A) None of the A. tumefaciens siblings is killed because of the presence of the Tdi immunity protein (orange or light green triangle) inactivating the injected Tde toxin from the WT. (B) With Δtae-tai lacking an amidase toxin-immunity pair (light blue), no killing occurs because Tae toxin is not the major antibacterial weapon during in planta colonization. (C) Injection of Tde toxin from WT A. tumefaciens to its sibling Δtde-tdi mutant (light blue) lacking the cognate immunity protein results in cell death caused by degradation of cellular DNA. (D) Injection of Tde toxin from WT A. tumefaciens to P. aeruginosa (pink) results in cell death caused by degradation of cellular DNA.

Figure 7

Conservation of Tde-Tdi Families in Bacteria (A) Representatives of the Tde family (shown in Figure 2A) from Gram (−) Proteobacteria and Bacteroidetes and Gram (+) Firmicutes and Actinobacteria phyla. The genetic organization is deducted from the genome context survey by BLASTP analysis and homologous genes are color-coded according to their known or predicted functions. The presence (indicated as T6SS+) or absence of T6SS (indicated as T6SS−) is based on the BLASTP analysis of the conserved T6SS components TssM, TssB, VgrG, and Hcp. (B) Eight classes of toxin_43 superfamily (PF15604). Proteins containing the toxin_43 domains are classified into eight classes/architectures according to the Pfam database. The graphical domain composition shows distinct domain organizations from a single to tandem toxin_43 domain fused to domains with known or unknown functions. The number of protein members found in each class is shown and classification of Tde1^At (A. tumefaciens Tde1) as class 1 and Tde2^At (A. tumefaciens Tde2) as class 3 is indicated. Detailed information for all class members and domain descriptions can be found in the Pfam PF15604 database (http://pfam.xfam.org/family/toxin_43). See also Figures S1, S3, S6, and S7.