Structure of a bacterial Rhs effector exported by the type VI secretion system

The type VI secretion system (T6SS) is a widespread protein export apparatus found in Gram-negative bacteria. The majority of T6SSs deliver toxic effector proteins into competitor bacteria. Yet, the structure, function, and activation of many of these effectors remains poorly understood. Here, we present the structures of the T6SS effector RhsA from Pseudomonas protegens and its cognate T6SS spike protein, VgrG1, at 3.3 Å resolution. The structures reveal that the rearrangement hotspot (Rhs) repeats of RhsA assemble into a closed anticlockwise β-barrel spiral similar to that found in bacterial insecticidal Tc toxins and in metazoan teneurin proteins. We find that the C-terminal toxin domain of RhsA is autoproteolytically cleaved but remains inside the Rhs ′cocoon′ where, with the exception of three ordered structural elements, most of the toxin is disordered. The N-terminal ′plug′ domain is unique to T6SS Rhs proteins and resembles a champagne cork that seals the Rhs cocoon at one end while also mediating interactions with VgrG1. Interestingly, this domain is also autoproteolytically cleaved inside the cocoon but remains associated with it. We propose that mechanical force is required to remove the cleaved part of the plug, resulting in the release of the toxin domain as it is delivered into a susceptible bacterial cell by the T6SS.

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Diversification of the Type VI Secretion System in Agrobacteria

mBio ◽

10.1128/mbio.01927-21 ◽

2021 ◽

Author(s):

Chih-Feng Wu ◽

Alexandra J. Weisberg ◽

Edward W. Davis ◽

Lin Chou ◽

Surtaz Khan ◽

...

Keyword(s):

Secretion System ◽

Effector Proteins ◽

Gram Negative Bacteria ◽

Type Vi Secretion System ◽

Gram Negative ◽

Bacterial Interactions ◽

Type Vi Secretion

The T6SS is used by several taxa of Gram-negative bacteria to secrete toxic effector proteins to attack others. Diversification of effector collections shapes bacterial interactions and impacts the health of hosts and ecosystems in which bacteria reside.

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Formylglycine-generating enzyme-like proteins constitute a novel family of widespread type VI secretion system immunity proteins

10.1101/2021.05.21.445229 ◽

2021 ◽

Author(s):

Juvenal Lopez ◽

Le Nguyen-Hung ◽

Ki Hwan Moon ◽

Dor Salomon ◽

Eran Bosis ◽

...

Keyword(s):

Protein Interactions ◽

Secretion System ◽

Effector Proteins ◽

Gram Negative Bacteria ◽

Dependent Manner ◽

Type Vi Secretion System ◽

Bacterial Killing ◽

Immunity Protein ◽

Gram Negative ◽

Type Vi Secretion

Competition is a critical aspect of bacterial life, as it enables niche establishment and facilitates the acquisition of essential nutrients. Warfare between Gram-negative bacteria is largely mediated by the type VI secretion system (T6SS), a dynamic nanoweapon that delivers toxic effector proteins from an attacking cell to adjacent bacteria in a contact-dependent manner. Effector-encoding bacteria prevent self-intoxication and kin cell killing by the expression of immunity proteins, which prevent effector toxicity by specifically binding their cognate effector and occluding its active site. In this study, we investigate Tsi3, a previously uncharacterized T6SS immunity protein present in multiple strains of the human pathogen Acinetobacter baumannii. We show that Tsi3 is the cognate immunity protein of the antibacterial effector of unknown function Tse3. Our bioinformatic analyses indicate that Tsi3 homologs are widespread among Gram-negative bacteria, often encoded within T6SS effector-immunity modules. Surprisingly, we found that Tsi3 homologs possess a characteristic formylglycine-generating enzyme (FGE) domain, which is present in various enzymatic proteins. Our data shows that Tsi3-mediated immunity is dependent on Tse3-Tsi3 protein-protein interactions and that Tsi3 homologs from various bacteria do not protect against Tse3-dependent bacterial killing. Thus, we conclude that Tsi3 homologs are unlikely to be functional enzymes. Collectively, our work identifies FGE domain-containing proteins as important mediators of immunity against T6SS attacks and indicates that the FGE domain can be co-opted as a scaffold in multiple proteins to carry out diverse functions.

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Formylglycine-generating enzyme-like proteins constitute a novel family of widespread type VI secretion system immunity proteins

Journal of Bacteriology ◽

10.1128/jb.00281-21 ◽

2021 ◽

Author(s):

Juvenal Lopez ◽

Nguyen-Hung Le ◽

Ki Hwan Moon ◽

Dor Salomon ◽

Eran Bosis ◽

...

Keyword(s):

Protein Interactions ◽

Secretion System ◽

Effector Proteins ◽

Gram Negative Bacteria ◽

Dependent Manner ◽

Type Vi Secretion System ◽

Bacterial Killing ◽

Immunity Protein ◽

Gram Negative ◽

Type Vi Secretion

Competition is a critical aspect of bacterial life, as it enables niche establishment and facilitates the acquisition of essential nutrients. Warfare between Gram-negative bacteria is largely mediated by the type VI secretion system (T6SS), a dynamic nanoweapon that delivers toxic effector proteins from an attacking cell to adjacent bacteria in a contact-dependent manner. Effector-encoding bacteria prevent self-intoxication and kin cell killing by the expression of immunity proteins, which prevent effector toxicity by specifically binding their cognate effector and either occluding its active site or preventing structural rearrangements necessary for effector activation. In this study, we investigate Tsi3, a previously uncharacterized T6SS immunity protein present in multiple strains of the human pathogen Acinetobacter baumannii . We show that Tsi3 is the cognate immunity protein of the antibacterial effector of unknown function Tse3. Our bioinformatic analyses indicate that Tsi3 homologs are widespread among Gram-negative bacteria, often encoded within T6SS effector-immunity modules. Surprisingly, we found that Tsi3 homologs are predicted to possess a characteristic formylglycine-generating enzyme (FGE) domain, which is present in various enzymatic proteins. Our data shows that Tsi3-mediated immunity is dependent on Tse3-Tsi3 protein-protein interactions and that Tsi3 homologs from various bacteria do not provide immunity against non-kin Tse3. Thus, we conclude that Tsi3 homologs are unlikely to be functional enzymes. Collectively, our work identifies FGE domain-containing proteins as important mediators of immunity against T6SS attacks and indicates that the FGE domain can be co-opted as a scaffold in multiple proteins to carry out diverse functions. Importance Despite the wealth of knowledge on the diversity of biochemical activities carried out by T6SS effectors, comparably little is known about the various strategies bacteria employ to prevent susceptibility to T6SS-dependent bacterial killing. Our work establishes a novel family of T6SS immunity proteins with a characteristic FGE domain. This domain is present in enzymatic proteins with various catalytic activities. Our characterization of Tsi3 expands the known functions carried out by FGE-like proteins to include defense during T6SS-mediated bacterial warfare. Moreover, it highlights the evolution of FGE domain-containing proteins to carry out diverse biological functions.

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Structure of a Peptidoglycan Amidase Effector Targeted to Gram-Negative Bacteria by the Type VI Secretion System

Cell Reports ◽

10.1016/j.celrep.2012.05.016 ◽

2012 ◽

Vol 1 (6) ◽

pp. 656-664 ◽

Cited By ~ 63

Author(s):

Seemay Chou ◽

Nhat Khai Bui ◽

Alistair B. Russell ◽

Katrina W. Lexa ◽

Taylor E. Gardiner ◽

...

Keyword(s):

Secretion System ◽

Gram Negative Bacteria ◽

Type Vi Secretion System ◽

Gram Negative ◽

Type Vi Secretion

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Bacterial Type VI secretion system could have evolved from co-opted tail sheath tube of bacteriophages

10.7287/peerj.preprints.27652v1 ◽

2019 ◽

Author(s):

Wenfa Ng

Keyword(s):

Protein Structure ◽

Bacterial Genome ◽

Secretion System ◽

Gram Negative Bacteria ◽

Bacterial Cells ◽

Type Vi Secretion System ◽

Gram Negative ◽

Type Vi Secretion ◽

Phage Tail ◽

Tail Protein

Bacterial cells utilize a variety of nanomachines to secrete proteins and other molecules into the extracellular environment or target cells. One example is the Type VI secretion system (T6SS) in Gram-negative bacteria. Armed with a contractile mechanism similar to that used by bacteriophages to inject phage DNA into bacterial cells, the T6SS shares a common evolutionary origin with tail associated proteins of bacteriophages at both the structural and protein composition levels. Specifically, proteins constituting the T6SS are known to share provenance with those of the phage tail protein. More importantly, the T6SS is strikingly similar to the phage tail protein in both structure and function. However, a more important question concerns whether the T6SS evolved from the phage tail protein and if yes, what is the mechanism responsible for its development? One possibility could be the co-opt of the tail protein structure by bacterial cells through integration of the genes encoding the tail protein structure within the bacterial genome. In this case, expression of the phage tail protein genes would have resulted in a multiprotein structure without apparent function, which meant that a significant gap remains in comparison with extant T6SS that spans the inner and outer cell membrane of Gram-negative bacteria. While it is desirable to trace the evolutionary steps taken by phage tail proteins to transform into functional T6SS, multiple selection pressure and strong mutational propensity might have erased molecular evidence of such transformation. Hence, the challenge lies in uncovering as much structural and sequence evidence as possible that points to distinct steps in the evolutionary pathway towards T6SS. Structural studies offer a particularly promising route to unentangle the details but it must be augmented with sequence evidence that pins down the molecular events that shape the evolution of the complex multiprotein structure, where clefts from one protein fit into the folds of another in yielding a function that could evolve over eons. Collectively, structural and functional similarity between T6SS and phage tail protein suggests a common evolutionary origin for both macromolecular complexes, which has been established through combined structural, compositional and sequence analysis. But the steps underpinning the transformation of phage tail protein into T6SS remain unclear, which obfuscate understanding of the evolutionary forces that shape the transformation. One possible evolutionary trajectory posits that genes expressing phage tail proteins were co-opted and integrated into the bacterial genome. However, significant gap remains between a phage tail protein structure with unclear function in the cytoplasm and a functional T6SS that spans two bacterial membranes. Future detective work at the structural and sequence level might offer clues to the evolutionary path trodden by a precursor of the bacterial T6SS.

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Killing of Gram-negative and Gram-positive bacteria by a bifunctional cell wall-targeting T6SS effector

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2106555118 ◽

2021 ◽

Vol 118 (40) ◽

pp. e2106555118

Author(s):

Nguyen-Hung Le ◽

Victor Pinedo ◽

Juvenal Lopez ◽

Felipe Cava ◽

Mario F. Feldman

Keyword(s):

Secretion System ◽

Bifunctional Enzyme ◽

Gram Negative Bacteria ◽

Type Vi Secretion System ◽

Gram Positive ◽

Gram Negative ◽

Bacterial Interactions ◽

Gram Positive Bacteria ◽

Lytic Transglycosylase ◽

Type Vi Secretion

The type VI secretion system (T6SS) is a powerful tool deployed by Gram-negative bacteria to antagonize neighboring organisms. Here, we report that Acinetobacter baumannii ATCC 17978 (Ab17978) secretes D-lysine (D-Lys), increasing the extracellular pH and enhancing the peptidoglycanase activity of the T6SS effector Tse4. This synergistic effect of D-Lys on Tse4 activity enables Ab17978 to outcompete Gram-negative bacterial competitors, demonstrating that bacteria can modify their microenvironment to increase their fitness during bacterial warfare. Remarkably, this lethal combination also results in T6SS-mediated killing of Gram-positive bacteria. Further characterization revealed that Tse4 is a bifunctional enzyme consisting of both lytic transglycosylase and endopeptidase activities, thus representing a family of modularly organized T6SS peptidoglycan-degrading effectors with an unprecedented impact in antagonistic bacterial interactions.

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Crystal structure of the Agrobacterium tumefaciens type VI effector–immunity complex

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x18016369 ◽

2018 ◽

Vol 74 (12) ◽

pp. 810-816 ◽

Cited By ~ 2

Author(s):

Satoshi Fukuhara ◽

Takanori Nakane ◽

Keitaro Yamashita ◽

Ryohei Ishii ◽

Ryuichiro Ishitani ◽

...

Keyword(s):

Agrobacterium Tumefaciens ◽

Three Dimensional ◽

Effector Proteins ◽

Gram Negative Bacteria ◽

Type Vi Secretion System ◽

Gram Negative ◽

Defense Systems ◽

Type Vi Secretion ◽

Inhibitory Mechanisms ◽

Microbial Defense

The type VI secretion system (T6SS) comprises needle-shaped multisubunit complexes that play a role in the microbial defense systems of Gram-negative bacteria. Some Gram-negative bacteria harboring a T6SS deliver toxic effector proteins into the cytoplasm or periplasm of competing bacteria in order to lyse and kill them. To avoid self-cell disruption, these bacteria have cognate immunity proteins that inhibit their toxic effector proteins. T6SS amidase effector protein 4 (Tae4) and T6SS amidase immunity protein 4 (Tai4) are a representative of the toxic effector–immunity pairs of the T6SS. Here, the three-dimensional structures of Tai4 and the Tae4–Tai4 complex from Agrobacterium tumefaciens are reported at 1.55 and 1.9 Å resolution, respectively. A structural comparison with other Tae4–Tai4 homologs revealed similarities and differences in the catalytic and inhibitory mechanisms among the Tae4 and Tai4 family proteins.

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TssA–TssM–TagA interaction modulates type VI secretion system sheath-tube assembly in Vibrio cholerae

Nature Communications ◽

10.1038/s41467-020-18807-9 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Maria Silvina Stietz ◽

Xiaoye Liang ◽

Hao Li ◽

Xinran Zhang ◽

Tao G. Dong

Keyword(s):

Genetic Mutation ◽

Secretion System ◽

Gram Negative Bacteria ◽

Type Vi Secretion System ◽

Physical Force ◽

Gram Negative ◽

Type Vi Secretion ◽

Protein Secretion System ◽

Membrane Spanning ◽

Tube Assembly

Abstract The type VI protein secretion system (T6SS) is a powerful needle-like machinery found in Gram-negative bacteria that can penetrate the cytosol of receiving cells in milliseconds by physical force. Anchored by its membrane-spanning complex (MC) and a baseplate (BP), the T6SS sheath-tube is assembled in a stepwise process primed by TssA and terminated by TagA. However, the molecular details of its assembly remain elusive. Here, we systematically examined the initiation and termination of contractile and non-contractile T6SS sheaths in MC-BP, tssA and tagA mutants by fluorescence microscopy. We observe long pole-to-pole sheath-tube structures in the non-contractile MC-BP defective mutants but not in the Hcp tube or VgrG spike mutants. Combining overexpression and genetic mutation data, we demonstrate complex effects of TssM, TssA and TagA interactions on T6SS sheath-tube dynamics. We also report promiscuous interactions of TagA with multiple T6SS components, similar to TssA. Our results demonstrate that priming of the T6SS sheath-tube assembly is not dependent on TssA, nor is the assembly termination dependent on the distal end TssA–TagA interaction, and highlight the tripartite control of TssA–TssM–TagA on sheath-tube initiation and termination.

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Structural Characterization of TssL from Acinetobacter baumannii: a Key Component of the Type VI Secretion System

Journal of Bacteriology ◽

10.1128/jb.00210-20 ◽

2020 ◽

Vol 202 (17) ◽

Author(s):

Federico M. Ruiz ◽

Juvenal Lopez ◽

C. Gastón Ferrara ◽

Elena Santillana ◽

Yanis R. Espinosa ◽

...

Keyword(s):

Acinetobacter Baumannii ◽

Secretion System ◽

Single Locus ◽

Gram Negative Bacteria ◽

Cytoplasmic Protein ◽

Type Vi Secretion System ◽

Inner Membrane ◽

Gram Negative ◽

Content Type ◽

Type Vi Secretion

ABSTRACT The type VI secretion system (T6SS) is a complex molecular nanomachine used by Gram-negative bacteria to deliver diverse effectors into adjacent cells. A membrane complex (MC) anchors this transport system to the bacterial cell wall. One of the proteins forming the MC is TssL, a cytoplasmic protein bound to the inner membrane through a single transmembrane helix. Here, we report the structure of the cytoplasmic N-terminal region of TssL from Acinetobacter baumannii, a bacterium encoding in a single locus a secretion system that is a special case among other T6SSs. The protein structure, consisting of two antiparallel alpha-helical bundles connected by a short loop, reveals several interesting particularities compared with homologous proteins from other organisms. In addition, we demonstrate the structural significance of residues Asp98 and Glu99, which are strongly conserved among T6SS-encoding Gram-negative bacteria. Mutations in these two residues strongly impact protein dynamics, expression, and functionality. Our results improve our understanding of the T6SS of A. baumannii, which remains largely understudied compared with that of other pathogens. IMPORTANCE Several Acinetobacter species carry one functional type VI secretion system (T6SS). The T6SS is encoded in a single locus containing 16 conserved genes, most of which code for proteins essential to T6SS activity. One of these key components is TssL, a cytoplasmic protein bound to the inner membrane. Despite its importance and its particular characteristics, the structure of T6SS in A. baumannii remains understudied. Here, we present structural, in silico, and in vivo studies of TssL, highlighting the importance of two well-conserved residues and improving our understanding of this secretion system in this bacterium.

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