scholarly journals Genome-wide prediction of bacterial effectors across six secretion system types using a feature-based supervised learning framework

2018 ◽  
Author(s):  
Andi Dhroso ◽  
Samantha Eidson ◽  
Dmitry Korkin
Keyword(s):  
Bacterial Infections ◽  
Molecular Mechanisms ◽  
Neglected Tropical Diseases ◽  
Secretion System ◽  
Effector Proteins ◽  
Gram Negative Bacteria ◽  
Secretion Systems ◽  
Gram Negative ◽  
Feature Based ◽  
Bacterial Effectors

AbstractGram-negative bacteria are responsible for hundreds of millions infections worldwide, including the emerging hospital-acquired infections and neglected tropical diseases in the third-world countries. Finding a fast and cheap way to understand the molecular mechanisms behind the bacterial infections is critical for efficient diagnostics and treatment. An important step towards understanding these mechanisms is discovering bacterial effectors, the proteins secreted into the host through one of the six common secretion system types. Unfortunately, current effector prediction methods are designed to specifically target one of three secretion systems, and no accurate “secretion system-agnostic” method is available.Here, we present PREFFECTOR, a computational feature-based approach to discover effectors in Gram-negative bacteria without prior knowledge on bacterial secretion system(s) or cryptic secretion signals. Our approach was first evaluated using several assessment protocols on a manually curated, balanced dataset of experimentally determined effectors across all six secretion systems as well as non-effector proteins. The evaluation revealed high accuracy of the top performing classifiers in PREFFECTOR, with the small false positive discovery rate across all six secretion systems. Our method was also applied to four bacteria that had limited knowledge on virulence factors or secreted effectors. PREFFECTOR web-server is freely available at: http://korkinlab.org/preffector.

scholarly journals Folding Control in the Path of Type 5 Secretion

Toxins ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 341
Author(s):  
Nathalie Dautin
Keyword(s):  
Protein Folding ◽  
Virulence Factors ◽  
Secretion System ◽  
Gram Negative Bacteria ◽  
Secretion Systems ◽  
Gram Negative ◽  
Final Destination ◽  
Cell Compartments ◽  
Recent Addition ◽  
Functionally Diverse

The type 5 secretion system (T5SS) is one of the more widespread secretion systems in Gram-negative bacteria. Proteins secreted by the T5SS are functionally diverse (toxins, adhesins, enzymes) and include numerous virulence factors. Mechanistically, the T5SS has long been considered the simplest of secretion systems, due to the paucity of proteins required for its functioning. Still, despite more than two decades of study, the exact process by which T5SS substrates attain their final destination and correct conformation is not totally deciphered. Moreover, the recent addition of new sub-families to the T5SS raises additional questions about this secretion mechanism. Central to the understanding of type 5 secretion is the question of protein folding, which needs to be carefully controlled in each of the bacterial cell compartments these proteins cross. Here, the biogenesis of proteins secreted by the Type 5 secretion system is discussed, with a focus on the various factors preventing or promoting protein folding during biogenesis.

scholarly journals Diversification of the Type VI Secretion System in Agrobacteria

mBio ◽  
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.

scholarly journals Intravenous Immunoglobulin for Treating Bacterial Infections: One More Mechanism of Action

2019 ◽  
Author(s):  
Teiji Sawa ◽  
Mao Kinoshita ◽  
Keita Inoue ◽  
Junya Ohara ◽  
Kiyoshi Moriyama
Keyword(s):  
Bacterial Infections ◽  
Bacterial Toxin ◽  
Resistant Bacteria ◽  
Gram Negative Bacteria ◽  
Secretion Systems ◽  
Gram Negative ◽  
Drug Resistant Bacteria ◽  
Toxin Secretion ◽  
Dependent Cell ◽  
V Antigen

The mechanisms underlying the effects of γ-globulin therapy for bacterial infections are thought to involve bacterial cell lysis via complement activation, phagocytosis via bacterial opsonization, toxin neutralization, and antibody-dependent cell-mediated cytotoxicity. Nevertheless, recent advances in the study of pathogenicity in gram-negative bacteria have raised the possibility of an association between γ-globulin and bacterial toxin secretion. Over time, new toxin secretion systems like the type III secretion system have been discovered in many pathogenic gram-negative bacteria. With this system, the bacterial toxins are directly injected into the cytoplasm of the target cell through a special secretory apparatus without any exposure to the extracellular environment and, therefore, with no opportunity for antibodies to neutralize the toxin. However, because antibodies against the V-antigen, which is located on the needle-shaped tip of the bacterial secretion apparatus, can inhibit toxin translocation, this raises the hope that the toxin might be susceptible to antibody targeting. Because multi-drug resistant bacteria are now prevalent, inhibiting this secretion mechanism is attractive as an alternative or adjunctive therapy against lethal bacterial infections. Thus, it would not be unreasonable to define the blocking effect of anti-V-antigen antibodies as the fifth mechanism for immunoglobulin action against bacterial infections.

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

2021 ◽  
Author(s):  
Patrick Guenther ◽  
Dennis Quentin ◽  
Shehryar Ahmad ◽  
Kartik Sachar ◽  
Christos Gatsogiannis ◽  
...  
Keyword(s):  
Bacterial Cell ◽  
Secretion System ◽  
Effector Proteins ◽  
Protein Export ◽  
Spike Protein ◽  
Gram Negative Bacteria ◽  
Structural Elements ◽  
Type Vi Secretion System ◽  
Gram Negative ◽  
Type Vi Secretion

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.

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

2022 ◽  
Vol 18 (1) ◽  
pp. e1010182
Author(s):  
Patrick Günther ◽  
Dennis Quentin ◽  
Shehryar Ahmad ◽  
Kartik Sachar ◽  
Christos Gatsogiannis ◽  
...  
Keyword(s):  
Bacterial Cell ◽  
Secretion System ◽  
Effector Proteins ◽  
Protein Export ◽  
Spike Protein ◽  
Gram Negative Bacteria ◽  
Structural Elements ◽  
Type Vi Secretion System ◽  
Gram Negative ◽  
Type Vi Secretion

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.

scholarly journals Immunoglobulin for Treating Bacterial Infections: One More Mechanism of Action

Antibodies ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 52 ◽  
Author(s):  
Sawa ◽  
Kinoshita ◽  
Inoue ◽  
Ohara ◽  
Moriyama
Keyword(s):  
Bacterial Infections ◽  
Bacterial Toxin ◽  
Resistant Bacteria ◽  
Attractive Alternative ◽  
Gram Negative Bacteria ◽  
Secretion Systems ◽  
Gram Negative ◽  
Drug Resistant Bacteria ◽  
Toxin Secretion ◽  
V Antigen

The mechanisms underlying the effects of immunoglobulins on bacterial infections are thought to involve bacterial cell lysis via complement activation, phagocytosis via bacterial opsonization, toxin neutralization, and antibody-dependent cell-mediated cytotoxicity. Nevertheless, recent advances in the study of the pathogenicity of Gram-negative bacteria have raised the possibility of an association between immunoglobulin and bacterial toxin secretion. Over time, new toxin secretion systems like the type III secretion system have been discovered in many pathogenic Gram-negative bacteria. With this system, the bacterial toxins are directly injected into the cytoplasm of the target cell through a special secretory apparatus without any exposure to the extracellular environment, and therefore with no opportunity for antibodies to neutralize the toxin. However, antibodies against the V-antigen, which is located on the needle-shaped tip of the bacterial secretion apparatus, can inhibit toxin translocation, thus raising the hope that the toxin may be susceptible to antibody targeting. Because multi-drug resistant bacteria are now prevalent, inhibiting this secretion mechanism is an attractive alternative or adjunctive therapy against lethal bacterial infections. Thus, it is not unreasonable to define the blocking effect of anti-V-antigen antibodies as the fifth mechanism for immunoglobulin action against bacterial infections.

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

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.

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

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.

scholarly journals Characterization of the Ruler Protein Interaction Interface on the Substrate Specificity Switch Protein in the Yersinia Type III Secretion System

2016 ◽  
Vol 292 (8) ◽  
pp. 3299-3311 ◽  
Author(s):  
Oanh Ho ◽  
Per Rogne ◽  
Tomas Edgren ◽  
Hans Wolf-Watz ◽  
Frédéric H. Login ◽  
...  
Keyword(s):  
Type Iii Secretion ◽  
Type Iii Secretion System ◽  
Secretion System ◽  
Effector Proteins ◽  
Host Cells ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Type Iii ◽  
Binding Interface ◽  
Interaction Interface

Many pathogenic Gram-negative bacteria use the type III secretion system (T3SS) to deliver effector proteins into eukaryotic host cells. In Yersinia, the switch to secretion of effector proteins is induced first after intimate contact between the bacterium and its eukaryotic target cell has been established, and the T3SS proteins YscP and YscU play a central role in this process. Here we identify the molecular details of the YscP binding site on YscU by means of nuclear magnetic resonance (NMR) spectroscopy. The binding interface is centered on the C-terminal domain of YscU. Disrupting the YscU-YscP interaction by introducing point mutations at the interaction interface significantly reduced the secretion of effector proteins and HeLa cell cytotoxicity. Interestingly, the binding of YscP to the slowly self-cleaving YscU variant P264A conferred significant protection against autoproteolysis. The YscP-mediated inhibition of YscU autoproteolysis suggests that the cleavage event may act as a timing switch in the regulation of early versus late T3SS substrates. We also show that YscUC binds to the inner rod protein YscI with a dissociation constant (Kd) of 3.8 μm and with 1:1 stoichiometry. The significant similarity among different members of the YscU, YscP, and YscI families suggests that the protein-protein interactions discussed in this study are also relevant for other T3SS-containing Gram-negative bacteria.

scholarly journals Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System

mBio ◽  
2010 ◽  
Vol 1 (3) ◽  
Author(s):  
Sarah Sanowar ◽  
Pragya Singh ◽  
Richard A. Pfuetzner ◽  
Ingemar André ◽  
Hongjin Zheng ◽  
...  
Keyword(s):  
Type Iii Secretion ◽  
Effector Proteins ◽  
Carboxyl Terminus ◽  
Gram Negative Bacteria ◽  
Secretion Systems ◽  
Gram Negative ◽  
Type Iii ◽  
Serovar Typhimurium ◽  
Cross Links ◽  
And Function

ABSTRACT The type III secretion system (T3SS) is an interspecies protein transport machine that plays a major role in interactions of Gram-negative bacteria with animals and plants by delivering bacterial effector proteins into host cells. T3SSs span both membranes of Gram-negative bacteria by forming a structure of connected oligomeric rings termed the needle complex (NC). Here, the localization of subunits in the Salmonella enterica serovar Typhimurium T3SS NC were probed via mass spectrometry-assisted identification of chemical cross-links in intact NC preparations. Cross-links between amino acids near the amino terminus of the outer membrane ring component InvG and the carboxyl terminus of the inner membrane ring component PrgH and between the two inner membrane components PrgH and PrgK allowed for spatial localization of the three ring components within the electron density map structures of NCs. Mutational and biochemical analysis demonstrated that the amino terminus of InvG and the carboxyl terminus of PrgH play a critical role in the assembly and function of the T3SS apparatus. Analysis of an InvG mutant indicates that the structure of the InvG oligomer can affect the switching of the T3SS substrate to translocon and effector components. This study provides insights into how structural organization of needle complex base components promotes T3SS assembly and function. IMPORTANCE Many biological macromolecular complexes are composed of symmetrical homomers, which assemble into larger structures. Some complexes, such as secretion systems, span biological membranes, forming hydrophilic domains to move substrates across lipid bilayers. Type III secretion systems (T3SSs) deliver bacterial effector proteins directly to the host cell cytoplasm and allow for critical interactions between many Gram-negative pathogenic bacterial species and their hosts. Progress has been made towards the goal of determining the three-dimensional structure of the secretion apparatus by determination of high-resolution crystal structures of individual protein subunits and low-resolution models of the assembly, using reconstructions of cryoelectron microscopy images. However, a more refined picture of the localization of periplasmic ring structures within the assembly and their interactions has only recently begun to emerge. This work localizes T3SS transmembrane rings and identifies structural elements that affect substrate switching and are essential to the assembly of components that are inserted into host cell membranes.

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