Role of Bacterial Secretion Systems and Effector Proteins – Insight into the Pathogenicity Mechanisms in Aeromonas

Gram-negative bacteria have developed several nanomachine channels known as type II, III, IV and VI secretion systems that enable export of effector proteins/toxins from the cytosol across the outer membrane to target host cells. Protein secretion systems are critical to bacterial virulence and interactions with other organisms. Aeromonas utilize various secretion machines e.g. two-step T2SS, a Sec-dependent system as well as one-step, Sec-independent T3SS and T6SS systems to transport effector proteins/toxins and virulence factors. Type III secretion system (T3SS) is considered the dominant virulence system in Aeromonas. The activity of bacterial T3SS effector proteins most often leads to disorders in signalling pathways and reorganization of the cell cytoskeleton. There are also scientific reports on the pathogenicity mechanism associated with host cell apopotosis/pyroptosis resulting from secretion of a cytotoxic enterotoxin, i.e. the Act protein, by the T2SS secretion system and an effector protein Hcp by the T6SS system. Type IV secretion system (T4SS) is the system which translocate protein substrates, protein-DNA complexes and DNA into eukaryotic or bacterial target cells. In this paper, the contribution of virulence determinants involved in the pathogenicity potential of Aeromonas is discussed. Considering that the variable expression of virulence factors has a decisive impact on the differences observed in the virulence of particular species of microorganisms, it is important to assess the correlation between bacterial pathogenicity and their virulence-associated genes.

Download Full-text

Postreplication Roles of theBrucellaVirB Type IV Secretion System Uncovered via Conditional Expression of the VirB11 ATPase

mBio ◽

10.1128/mbio.01730-16 ◽

2016 ◽

Vol 7 (6) ◽

Cited By ~ 17

Author(s):

Erin P. Smith ◽

Cheryl N. Miller ◽

Robert Child ◽

Jennifer A. Cundiff ◽

Jean Celli

Keyword(s):

Brucella Abortus ◽

Secretion System ◽

Effector Proteins ◽

Type Iv Secretion ◽

Host Cells ◽

Type Iv Secretion System ◽

Secretion Systems ◽

Type Iv ◽

Conditional Expression ◽

Bacterial Replication

ABSTRACTBrucella abortus, the bacterial agent of the worldwide zoonosis brucellosis, primarily infects host phagocytes, where it undergoes an intracellular cycle within a dedicated membrane-bound vacuole, theBrucella-containing vacuole (BCV). Initially of endosomal origin (eBCV), BCVs are remodeled into replication-permissive organelles (rBCV) derived from the host endoplasmic reticulum, a process that requires modulation of host secretory functions via delivery of effector proteins by theBrucellaVirB type IV secretion system (T4SS). Following replication, rBCVs are converted into autophagic vacuoles (aBCVs) that facilitate bacterial egress and subsequent infections, arguing that the bacterium sequentially manipulates multiple cellular pathways to complete its cycle. The VirB T4SS is essential for rBCV biogenesis, as VirB-deficient mutants are stalled in eBCVs and cannot mediate rBCV biogenesis. This has precluded analysis of whether the VirB apparatus also drives subsequent stages of theBrucellaintracellular cycle. To address this issue, we have generated aB. abortusstrain in which VirB T4SS function is conditionally controlled via anhydrotetracycline (ATc)-dependent complementation of a deletion of thevirB11gene encoding the VirB11 ATPase. We show in murine bone marrow-derived macrophages (BMMs) that early VirB production is essential for optimal rBCV biogenesis and bacterial replication. Transient expression ofvirB11prior to infection was sufficient to mediate normal rBCV biogenesis and bacterial replication but led to T4SS inactivation and decreased aBCV formation and bacterial release, indicating that these postreplication stages are also T4SS dependent. Hence, our findings support the hypothesis of additional, postreplication roles of type IV secretion in theBrucellaintracellular cycle.IMPORTANCEMany intracellular bacterial pathogens encode specialized secretion systems that deliver effector proteins into host cells to mediate the multiple stages of their intracellular cycles. Because these intracellular events occur sequentially, classical genetic approaches cannot address the late roles that these apparatuses play, as secretion-deficient mutants cannot proceed past their initial defect. Here we have designed a functionally controllable VirB type IV secretion system (T4SS) in the bacterial pathogenBrucella abortusto decipher its temporal requirements during the bacterium’s intracellular cycle in macrophages. By controlling production of the VirB11 ATPase, which energizes the T4SS, we show not only that this apparatus is required early to generate theBrucellareplicative organelle but also that it contributes to completion of the bacterium’s cycle and bacterial egress. Our findings expand upon the pathogenic functions of theBrucellaVirB T4SS and illustrate targeting of secretion ATPases as a useful strategy to manipulate the activity of bacterial secretion systems.

Download Full-text

Acinetobacter baumannii: Resistance and Virulence mediated through bacterial type IV secretion system

Revista Estomatología ◽

10.25100/re.v21i2.5765 ◽

2017 ◽

Vol 21 (2) ◽

pp. 37-45

Author(s):

Andrés Zúñiga-Bahamon ◽

Fabián Tobar ◽

Juan Fernando Duque ◽

Pedro Moreno

Keyword(s):

Bacterial Resistance ◽

Genetic Material ◽

Secretion System ◽

Effector Proteins ◽

Type Iv Secretion ◽

Host Cells ◽

Secretion Systems ◽

Type Iv ◽

Bacterial Secretion ◽

Bacterial Type

Introduction: Type IV Bacterial Secretion Systems (TFSS) have a variety of biological functions such as the exchange of genetic material with other bacteria and virulent translocation of DNA with its effector proteins into host cells. A. baumannii is a pathogen that causes infections in humans and exhibits high rates of multidrug resistance to drugs. Objective: To relate how type IV secretion systems is associated with patterns of resistance and virulence in A. baumannii. Materials and Methods: Exhaustive search in PMC (NCBI) using a set of keywords was performed. Results: The search yielded 133 articles. Fourteen articles were analysed to determine the bacterial secretion system and the resistant and virulence of AA. baumannii. Conclusions: Systems of bacterial type IV secretion present in A. baumannii are crucial in understanding the patterns of virulence and resistance. Key words: Pathogenicity, type four secretion system (T4SS), A. baumannii, virulence factors, multidrug bacterial resistance (MDR), horizontal gene transfer (HGT).

Download Full-text

Peptidomimetic Small Molecules Disrupt Type IV Secretion System Activity in Diverse Bacterial Pathogens

mBio ◽

10.1128/mbio.00221-16 ◽

2016 ◽

Vol 7 (2) ◽

Cited By ~ 22

Author(s):

Carrie L. Shaffer ◽

James A. D. Good ◽

Santosh Kumar ◽

K. Syam Krishnan ◽

Jennifer A. Gaddy ◽

...

Keyword(s):

Antibiotic Resistance ◽

Small Molecules ◽

Bacterial Pathogens ◽

Effector Proteins ◽

Type Iv Secretion ◽

Target Cells ◽

Effector Protein ◽

Secretion Systems ◽

Type Iv ◽

H Pylori

ABSTRACT Bacteria utilize complex type IV secretion systems (T4SSs) to translocate diverse effector proteins or DNA into target cells. Despite the importance of T4SSs in bacterial pathogenesis, the mechanism by which these translocation machineries deliver cargo across the bacterial envelope remains poorly understood, and very few studies have investigated the use of synthetic molecules to disrupt T4SS-mediated transport. Here, we describe two synthetic small molecules (C10 and KSK85) that disrupt T4SS-dependent processes in multiple bacterial pathogens. Helicobacter pylori exploits a pilus appendage associated with the cag T4SS to inject an oncogenic effector protein (CagA) and peptidoglycan into gastric epithelial cells. In H. pylori , KSK85 impedes biogenesis of the pilus appendage associated with the cag T4SS, while C10 disrupts cag T4SS activity without perturbing pilus assembly. In addition to the effects in H. pylori , we demonstrate that these compounds disrupt interbacterial DNA transfer by conjugative T4SSs in Escherichia coli and impede vir T4SS-mediated DNA delivery by Agrobacterium tumefaciens in a plant model of infection. Of note, C10 effectively disarmed dissemination of a derepressed IncF plasmid into a recipient bacterial population, thus demonstrating the potential of these compounds in mitigating the spread of antibiotic resistance determinants driven by conjugation. To our knowledge, this study is the first report of synthetic small molecules that impair delivery of both effector protein and DNA cargos by diverse T4SSs. IMPORTANCE Many human and plant pathogens utilize complex nanomachines called type IV secretion systems (T4SSs) to transport proteins and DNA to target cells. In addition to delivery of harmful effector proteins into target cells, T4SSs can disseminate genetic determinants that confer antibiotic resistance among bacterial populations. In this study, we sought to identify compounds that disrupt T4SS-mediated processes. Using the human gastric pathogen H. pylori as a model system, we identified and characterized two small molecules that prevent transfer of an oncogenic effector protein to host cells. We discovered that these small molecules also prevented the spread of antibiotic resistance plasmids in E. coli populations and diminished the transfer of tumor-inducing DNA from the plant pathogen A. tumefaciens to target cells. Thus, these compounds are versatile molecular tools that can be used to study and disarm these important bacterial machines.

Download Full-text

Membrane and Core Periplasmic Agrobacterium tumefaciens Virulence Type IV Secretion System Components Localize to Multiple Sites around the Bacterial Perimeter during Lateral Attachment to Plant Cells

mBio ◽

10.1128/mbio.00218-11 ◽

2011 ◽

Vol 2 (6) ◽

Cited By ~ 33

Author(s):

Julieta Aguilar ◽

Todd A. Cameron ◽

John Zupan ◽

Patricia Zambryski

Keyword(s):

Agrobacterium Tumefaciens ◽

Plant Cells ◽

Secretion System ◽

Type Iv Secretion ◽

Host Cells ◽

Type Iv Secretion System ◽

Secretion Systems ◽

Content Type ◽

Protein Substrates ◽

Type Iv

ABSTRACTType IV secretion systems (T4SS) transfer DNA and/or proteins into recipient cells. Here we performed immunofluorescence deconvolution microscopy to localize the assembled T4SS by detection of its native components VirB1, VirB2, VirB4, VirB5, VirB7, VirB8, VirB9, VirB10, and VirB11 in the C58 nopaline strain ofAgrobacterium tumefaciens, following induction of virulence (vir) gene expression. These different proteins represent T4SS components spanning the inner membrane, periplasm, or outer membrane. Native VirB2, VirB5, VirB7, and VirB8 were also localized in theA. tumefaciensoctopine strain A348. Quantitative analyses of the localization of all the above Vir proteins in nopaline and octopine strains revealed multiple foci in single optical sections in over 80% and 70% of the bacterial cells, respectively. Green fluorescent protein (GFP)-VirB8 expression followingvirinduction was used to monitor bacterial binding to live host plant cells; bacteria bind predominantly along their lengths, with few bacteria binding via their poles or subpoles.vir-induced attachment-defective bacteria or bacteria without the Ti plasmid do not bind to plant cells. These data support a model where multiplevir-T4SS around the perimeter of the bacterium maximize effective contact with the host to facilitate efficient transfer of DNA and protein substrates.IMPORTANCETransfer of DNA and/or proteins to host cells through multiprotein type IV secretion system (T4SS) complexes that span the bacterial cell envelope is critical to bacterial pathogenesis. Early reports suggested that T4SS components localized at the cell poles. Now, higher-resolution deconvolution fluorescence microscopy reveals that all structural components of theAgrobacterium tumefaciens vir-T4SS, as well as its transported protein substrates, localize to multiple foci around the cell perimeter. These results lead to a new model ofA. tumefaciensattachment to a plant cell, whereA. tumefacienstakes advantage of the multiplevir-T4SS along its length to make intimate lateral contact with plant cells and thereby effectively transfer DNA and/or proteins through thevir-T4SS. The T4SS ofA. tumefaciensis among the best-studied T4SS, and the majority of its components are highly conserved in different pathogenic bacterial species. Thus, the results presented can be applied to a broad range of pathogens that utilize T4SS.

Download Full-text

Molecular and Structural Analysis of the Helicobacter pylori cag Type IV Secretion System Core Complex

mBio ◽

10.1128/mbio.02001-15 ◽

2016 ◽

Vol 7 (1) ◽

Cited By ~ 67

Author(s):

Arwen E. Frick-Cheng ◽

Tasia M. Pyburn ◽

Bradley J. Voss ◽

W. Hayes McDonald ◽

Melanie D. Ohi ◽

...

Keyword(s):

Helicobacter Pylori ◽

Bacterial Species ◽

Secretion System ◽

Effector Proteins ◽

Type Iv Secretion ◽

Secretion Systems ◽

Core Complex ◽

Type Iv ◽

Membrane Spanning ◽

H Pylori

ABSTRACT Bacterial type IV secretion systems (T4SSs) can function to export or import DNA, and can deliver effector proteins into a wide range of target cells. Relatively little is known about the structural organization of T4SSs that secrete effector proteins. In this report, we describe the isolation and analysis of a membrane-spanning core complex from the Helicobacter pylori cag T4SS, which has an important role in the pathogenesis of gastric cancer. We show that this complex contains five H. pylori proteins, CagM, CagT, Cag3, CagX, and CagY, each of which is required for cag T4SS activity. CagX and CagY are orthologous to the VirB9 and VirB10 components of T4SSs in other bacterial species, and the other three Cag proteins are unique to H. pylori . Negative stain single-particle electron microscopy revealed complexes 41 nm in diameter, characterized by a 19-nm-diameter central ring linked to an outer ring by spoke-like linkers. Incomplete complexes formed by Δ cag3 or Δ cagT mutants retain the 19-nm-diameter ring but lack an organized outer ring. Immunogold labeling studies confirm that Cag3 is a peripheral component of the complex. The cag T4SS core complex has an overall diameter and structural organization that differ considerably from the corresponding features of conjugative T4SSs. These results highlight specialized features of the H. pylori cag T4SS that are optimized for function in the human gastric mucosal environment. IMPORTANCE Type IV secretion systems (T4SSs) are versatile macromolecular machines that are present in many bacterial species. In this study, we investigated a T4SS found in the bacterium Helicobacter pylori. H. pylori is an important cause of stomach cancer, and the H. pylori T4SS contributes to cancer pathogenesis by mediating entry of CagA (an effector protein regarded as a “bacterial oncoprotein”) into gastric epithelial cells. We isolated and analyzed the membrane-spanning core complex of the H. pylori T4SS and showed that it contains unique proteins unrelated to components of T4SSs in other bacterial species. These results constitute the first structural analysis of the core complex from this important secretion system.

Download Full-text

DeepT3_4: A Hybrid Deep Neural Network Model for the Distinction Between Bacterial Type III and IV Secreted Effectors

Frontiers in Microbiology ◽

10.3389/fmicb.2021.605782 ◽

2021 ◽

Vol 12 ◽

Author(s):

Lezheng Yu ◽

Fengjuan Liu ◽

Yizhou Li ◽

Jiesi Luo ◽

Runyu Jing

Keyword(s):

Neural Network ◽

Neural Networks ◽

Secretion System ◽

Effector Proteins ◽

Host Cells ◽

Sequence Motifs ◽

Type Vi Secretion System ◽

Type Iii ◽

Type Iv

Gram-negative bacteria can deliver secreted proteins (also known as secreted effectors) directly into host cells through type III secretion system (T3SS), type IV secretion system (T4SS), and type VI secretion system (T6SS) and cause various diseases. These secreted effectors are heavily involved in the interactions between bacteria and host cells, so their identification is crucial for the discovery and development of novel anti-bacterial drugs. It is currently challenging to accurately distinguish type III secreted effectors (T3SEs) and type IV secreted effectors (T4SEs) because neither T3SEs nor T4SEs contain N-terminal signal peptides, and some of these effectors have similar evolutionary conserved profiles and sequence motifs. To address this challenge, we develop a deep learning (DL) approach called DeepT3_4 to correctly classify T3SEs and T4SEs. We generate amino-acid character dictionary and sequence-based features extracted from effector proteins and subsequently implement these features into a hybrid model that integrates recurrent neural networks (RNNs) and deep neural networks (DNNs). After training the model, the hybrid neural network classifies secreted effectors into two different classes with an accuracy, F-value, and recall of over 80.0%. Our approach stands for the first DL approach for the classification of T3SEs and T4SEs, providing a promising supplementary tool for further secretome studies.

Download Full-text

Using an Optimal Set of Features with a Machine Learning-Based Approach to Predict Effector Proteins forLegionella pneumophila

10.1101/383570 ◽

2018 ◽

Author(s):

Zhila Esna Ashari ◽

Kelly A. Brayton ◽

Shira L. Broschat

Keyword(s):

Machine Learning ◽

Legionella Pneumophila ◽

De Novo ◽

Effector Proteins ◽

Machine Learning Algorithms ◽

Host Cells ◽

Support Vector ◽

Secretion Systems ◽

Type Iv ◽

Optimal Set

AbstractType IV secretion systems exist in a number of bacterial pathogens and are used to secrete effector proteins directly into host cells in order to change their environment making the environment hospitable for the bacteria. In recent years, several machine learning algorithms have been developed to predict effector proteins, potentially facilitating experimental verification. However, inconsistencies exist between their results. Previously we analysed the disparate sets of predictive features used in these algorithms to determine an optimal set of 370 features for effector prediction. This work focuses on the best way to use these optimal features by designing three machine learning classifiers, comparing our results with those of others, and obtaining de novo results. We chose the pathogenLegionella pneumophilastrain Philadelphia-1, a cause of Legionnaires’ disease, because it has many validated effector proteins and others have developed machine learning prediction tools for it. While all of our models give good results indicating that our optimal features are quite robust, Model 1, which uses all 370 features with a support vector machine, has slightly better accuracy. Moreover, Model 1 predicted 760 effector proteins, more than any other study, 315 of which have been validated. Although the results of our three models agree well with those of other researchers, their models only predicted 126 and 311 candidate effectors.

Download Full-text

The Impact of Bartonella VirB/VirD4 Type IV Secretion System Effectors on Eukaryotic Host Cells

Frontiers in Microbiology ◽

10.3389/fmicb.2021.762582 ◽

2021 ◽

Vol 12 ◽

Author(s):

Katja Fromm ◽

Christoph Dehio

Keyword(s):

Current Knowledge ◽

Secretion System ◽

Effector Proteins ◽

Type Iv Secretion ◽

Host Cells ◽

Type Iv Secretion System ◽

Type Iv ◽

Wide Range ◽

Host Signaling ◽

The Impact

Bartonella spp. are facultative intracellular pathogens that infect a wide range of mammalian hosts including humans. The VirB/VirD4 type IV secretion system (T4SS) is a key virulence factor utilized to translocate Bartonella effector proteins (Beps) into host cells in order to subvert their functions. Crucial for effector translocation is the C-terminal Bep intracellular delivery (BID) domain that together with a positively charged tail sequence forms a bipartite translocation signal. Multiple BID domains also evolved secondary effector functions within host cells. The majority of Beps possess an N-terminal filamentation induced by cAMP (FIC) domain and a central connecting oligonucleotide binding (OB) fold. FIC domains typically mediate AMPylation or related post-translational modifications of target proteins. Some Beps harbor other functional modules, such as tandem-repeated tyrosine-phosphorylation (EPIYA-related) motifs. Within host cells the EPIYA-related motifs are phosphorylated, which facilitates the interaction with host signaling proteins. In this review, we will summarize our current knowledge on the molecular functions of the different domains present in Beps and highlight examples of Bep-dependent host cell modulation.

Download Full-text

Legionella pneumophila Strain 130b Possesses a Unique Combination of Type IV Secretion Systems and Novel Dot/Icm Secretion System Effector Proteins

Journal of Bacteriology ◽

10.1128/jb.00778-10 ◽

2010 ◽

Vol 192 (22) ◽

pp. 6001-6016 ◽

Cited By ~ 81

Author(s):

Gunnar N. Schroeder ◽

Nicola K. Petty ◽

Aurélie Mousnier ◽

Clare R. Harding ◽

Adam J. Vogrin ◽

...

Keyword(s):

Legionella Pneumophila ◽

Draft Genome ◽

Severe Pneumonia ◽

Gene Clusters ◽

Secretion System ◽

Effector Proteins ◽

Type Iv Secretion ◽

Secretion Systems ◽

Type Iv ◽

Core Set

ABSTRACT Legionella pneumophila is a ubiquitous inhabitant of environmental water reservoirs. The bacteria infect a wide variety of protozoa and, after accidental inhalation, human alveolar macrophages, which can lead to severe pneumonia. The capability to thrive in phagocytic hosts is dependent on the Dot/Icm type IV secretion system (T4SS), which translocates multiple effector proteins into the host cell. In this study, we determined the draft genome sequence of L. pneumophila strain 130b (Wadsworth). We found that the 130b genome encodes a unique set of T4SSs, namely, the Dot/Icm T4SS, a Trb-1-like T4SS, and two Lvh T4SS gene clusters. Sequence analysis substantiated that a core set of 107 Dot/Icm T4SS effectors was conserved among the sequenced L. pneumophila strains Philadelphia-1, Lens, Paris, Corby, Alcoy, and 130b. We also identified new effector candidates and validated the translocation of 10 novel Dot/Icm T4SS effectors that are not present in L. pneumophila strain Philadelphia-1. We examined the prevalence of the new effector genes among 87 environmental and clinical L. pneumophila isolates. Five of the new effectors were identified in 34 to 62% of the isolates, while less than 15% of the strains tested positive for the other five genes. Collectively, our data show that the core set of conserved Dot/Icm T4SS effector proteins is supplemented by a variable repertoire of accessory effectors that may partly account for differences in the virulences and prevalences of particular L. pneumophila strains.

Download Full-text

T4SS Effector Protein Prediction with Deep Learning

Data ◽

10.3390/data4010045 ◽

2019 ◽

Vol 4 (1) ◽

pp. 45 ◽

Cited By ~ 2

Author(s):

Koray Açıcı ◽

Tunç Aşuroğlu ◽

Çağatay Erdaş ◽

Hasan Oğul

Keyword(s):

Deep Learning ◽

Extraction Methods ◽

Effector Proteins ◽

Machine Learning Algorithms ◽

Host Cells ◽

Correct Prediction ◽

Human Pathogens ◽

Secretion Systems ◽

Type Iv ◽

Protein Prediction

Extensive research has been carried out on bacterial secretion systems, as they can pass effector proteins directly into the cytoplasm of host cells. The correct prediction of type IV protein effectors secreted by T4SS is important, since they are known to play a noteworthy role in various human pathogens. Studies on predicting T4SS effectors involve traditional machine learning algorithms. In this work we included a deep learning architecture, i.e., a Convolutional Neural Network (CNN), to predict IVA and IVB effectors. Three feature extraction methods were utilized to represent each protein as an image and these images fed the CNN as inputs in our proposed framework. Pseudo proteins were generated using ADASYN algorithm to overcome the imbalanced dataset problem. We demonstrated that our framework predicted all IVA effectors correctly. In addition, the sensitivity performance of 94.2% for IVB effector prediction exhibited our framework’s ability to discern the effectors in unidentified proteins.

Download Full-text