scholarly journals Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Hong Li ◽  
Xiang Ma ◽  
Yanqiong Tang ◽  
Dan Wang ◽  
Ziding Zhang ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Bacterial Pathogen ◽  
Signal Transduction Pathway ◽  
Immune Defense ◽  
Ppi Network ◽  
Host Proteins ◽  
Homologous Proteins ◽  
Aeromonas Veronii ◽  
Regulatory Systems ◽  
Network Modules

Abstract Background Aeromonas veronii is a bacterial pathogen in aquaculture, which produces virulence factors to enable it colonize and evade host immune defense. Given that experimental verification of virulence factors is time-consuming and laborious, few virulence factors have been characterized. Moreover, most studies have only focused on single virulence factors, resulting in biased interpretation of the pathogenesis of A. veronii. Results In this study, a PPI network at genome-wide scale for A. veronii was first constructed followed by prediction and mapping of virulence factors on the network. When topological characteristics were analyzed, the virulence factors had higher degree and betweenness centrality than other proteins in the network. In particular, the virulence factors tended to interact with each other and were enriched in two network modules. One of the modules mainly consisted of histidine kinases, response regulators, diguanylate cyclases and phosphodiesterases, which play important roles in two-component regulatory systems and the synthesis and degradation of cyclic-diGMP. Construction of the interspecies PPI network between A. veronii and its host Oreochromis niloticus revealed that the virulence factors interacted with homologous proteins in the host. Finally, the structures and interacting sites of the virulence factors during interaction with host proteins were predicted. Conclusions The findings here indicate that the virulence factors probably regulate the virulence of A. veronii by involving in signal transduction pathway and manipulate host biological processes by mimicking and binding competitively to host proteins. Our results give more insight into the pathogenesis of A. veronii and provides important information for designing targeted antibacterial drugs.

scholarly journals Network-Based Analysis of Virulence Factors for Uncovering Aeromonas Veronii Pathogenesis

2021 ◽  
Author(s):  
Hong Li ◽  
Xiang Ma ◽  
Yanqiong Tang ◽  
Dan Wang ◽  
Ziding Zhang ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Signal Transduction Pathway ◽  
Ppi Network ◽  
Host Proteins ◽  
Protein Protein Interaction ◽  
Aeromonas Veronii ◽  
Regulatory Systems ◽  
Diguanylate Cyclases ◽  
Network Modules ◽  
Wide Scale

Abstract Background: Aeromonas veronii is a pathogen that causes serious harm to aquaculture. Virulence factors are its pathogenic basis, which could promote pathogens to colonize the host, evade host defense and so on. But because experimental verification of virulence factors is time-consuming and laborious, the number of known virulence factors is limited. In this past, most studies only focused on single virulence factor, resulting the biased interpretation for pathogenesis.Results: In this study, a protein-protein interaction (PPI) network at genome-wide scale for A. veronii was first constructed. Then, virulence factors were predicted and mapped on the network. Topological characteristics of the virulence factors were analyzed. The results showed that the virulence factors had higher degree and betweenness centrality than the other proteins in the network. In particular, the virulence factors tended to interact with each other and were enriched in two network modules. One of the modules mainly consisted of histidine kinases, response regulators, diguanylate cyclases and phosphodiesterases, which played important roles in two-component regulatory systems and the synthesis and degradation of cyclic-diGMP. Furthermore, an interspecies PPI network between A. veronii and its host Oreochromis niloticus was also constructed. The structures and interacting sites of the virulence factors and host proteins were added to the interspecies PPI network. By analyzing the interspecies PPI network, we found that the virulence factors could competitively bind host proteins and some of the interacting sites of the virulence factors were shared by different host proteins. Drugs could be designed to target these sites and further prevent pathogen to interfere with host pathways.Conclusions: Our results indicated that the virulence factors regulated the virulence of A. veronii by involving in signal transduction pathway and manipulate host biological processes by mimicking and competitively binding host proteins. Our results deepened the understanding for pathogenesis and had important theoretical significance for designing targeted antibacterial drugs.

scholarly journals Revisiting the quorum-sensing hierarchy in Pseudomonas aeruginosa: the transcriptional regulator RhlR regulates LasR-specific factors

Microbiology ◽  
2009 ◽  
Vol 155 (3) ◽  
pp. 712-723 ◽  
Author(s):  
Valérie Dekimpe ◽  
Eric Déziel
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Quorum Sensing ◽  
Virulence Factors ◽  
Transcriptional Regulator ◽  
Homoserine Lactone ◽  
The Other ◽  
Virulence Determinants ◽  
Late Stationary Phase ◽  
Regulatory Systems ◽  
Specific Factors

Pseudomonas aeruginosa uses the two major quorum-sensing (QS) regulatory systems las and rhl to modulate the expression of many of its virulence factors. The las system is considered to stand at the top of the QS hierarchy. However, some virulence factors such as pyocyanin have been reported to still be produced in lasR mutants under certain conditions. Interestingly, such mutants arise spontaneously under various conditions, including in the airways of cystic fibrosis patients. Using transcriptional lacZ reporters, LC/MS quantification and phenotypic assays, we have investigated the regulation of QS-controlled factors by the las system. Our results show that activity of the rhl system is only delayed in a lasR mutant, thus allowing the expression of multiple virulence determinants such as pyocyanin, rhamnolipids and C4-homoserine lactone (HSL) during the late stationary phase. Moreover, at this stage, RhlR is able to overcome the absence of the las system by activating specific LasR-controlled functions, including production of 3-oxo-C12-HSL and Pseudomonas quinolone signal (PQS). P. aeruginosa is thus able to circumvent the deficiency of one of its QS systems by allowing the other to take over. This work demonstrates that the QS hierarchy is more complex than the model simply presenting the las system above the rhl system.

scholarly journals Network-Guided Discovery of Influenza Virus Replication Host Factors

mBio ◽  
2018 ◽  
Vol 9 (6) ◽  
Author(s):  
Emily E. Ackerman ◽  
Eiryo Kawakami ◽  
Manami Katoh ◽  
Tokiko Watanabe ◽  
Shinji Watanabe ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Viral Replication ◽  
Virus Replication ◽  
Drug Targets ◽  
Antiviral Drug ◽  
Viral Proteins ◽  
Host Factors ◽  
Ppi Network ◽  
Host Proteins ◽  
Influenza Virus Replication

ABSTRACTThe positions of host factors required for viral replication within a human protein-protein interaction (PPI) network can be exploited to identify drug targets that are robust to drug-mediated selective pressure. Host factors can physically interact with viral proteins, be a component of virus-regulated pathways (where proteins do not interact with viral proteins), or be required for viral replication but unregulated by viruses. Here, we demonstrate a method of combining human PPI networks with virus-host PPI data to improve antiviral drug discovery for influenza viruses by identifying target host proteins. Analysis shows that influenza virus proteins physically interact with host proteins in network positions significant for information flow, even after the removal of known abundance-degree bias within PPI data. We have isolated a subnetwork of the human PPI network that connects virus-interacting host proteins to host factors that are important for influenza virus replication without physically interacting with viral proteins. The subnetwork is enriched for signaling and immune processes distinct from those associated with virus-interacting proteins. Selecting proteins based on subnetwork topology, we performed an siRNA screen to determine whether the subnetwork was enriched for virus replication host factors and whether network position within the subnetwork offers an advantage in prioritization of drug targets to control influenza virus replication. We found that the subnetwork is highly enriched for target host proteins—more so than the set of host factors that physically interact with viral proteins. Our findings demonstrate that network positions are a powerful predictor to guide antiviral drug candidate prioritization.IMPORTANCEIntegrating virus-host interactions with host protein-protein interactions, we have created a method using these established network practices to identify host factors (i.e., proteins) that are likely candidates for antiviral drug targeting. We demonstrate that interaction cascades between host proteins that directly interact with viral proteins and host factors that are important to influenza virus replication are enriched for signaling and immune processes. Additionally, we show that host proteins that interact with viral proteins are in network locations of power. Finally, we demonstrate a new network methodology to predict novel host factors and validate predictions with an siRNA screen. Our results show that integrating virus-host proteins interactions is useful in the identification of antiviral drug target candidates.

scholarly journals MODERN APPROACHES TO ANTIVIRULENT THERAPY OF DISEASES ASSOCIATED WITH STAPHYLOCOCCUS AUREUS

2019 ◽  
Vol 23 (3-4) ◽  
pp. 26-31
Author(s):  
T.O. Kryuchko ◽  
O.Ya. Tkachenko ◽  
N.V. Kuzmenko ◽  
I.N. Nesina ◽  
S.M. Tanianska ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Virulence Factors ◽  
Bacterial Infections ◽  
Effective Means ◽  
Bacterial Pathogen ◽  
Cross Reactivity ◽  
Main Function ◽  
Virulence Proteins ◽  
New Antibiotics ◽  
Active Research

Staphylococcus aureus is a universal bacterial pathogen, which is able to develop the resistance to new antibiotics, by means of virulence factors, whose main function is the spread of diseases by inhibiting the immune factors of host defense. Its wide spread at in-patient departments and also the presence of clinical probationary wards Staphylococcus aureus, resistant to methicillin at out-patient departments, deprive the doctors of effective means for control of the infection. Complications caused by MRSA lead to hospitalization and indices of lethality. The aim of the paper is to analyze the main factors of S. аureus virulence and ways the of its interaction as a result of etiological and pathogenetic treatment. Complexity of treatment of bacterial infections is determined by alternative ways of prevention and treatment of diseases to which bacteria are not able to develop resistance. Along with general mechanisms that form antibiotic resistance, S. aureus produces many individual virulence factors that model the immune response, affecting the survival of the microorganism. The virulence factors produced by S. aureus are diverse and have the ability not only to cause cell lysis, but also to stimulate tissue rejection and destruction. It is important to determine that many specific factors of virulence caused by S. aureus, have ability to change both congenital and adaptive immune reactions including inhibition of complement activation, neutrophils neutralization, phagocytes inhibition. Strategies for inhibiting virulence factors can range from using small inhibitor molecules or full-fledged antibodies to creating toxoids and virulence proteins. Great interest is focused upon those inhibitors that have cross-reactivity with respect to multiple virulence factors, as well as inhibitors, the main target of which is a global regulator with multi-purpose activity, for example, agr operon. Active research into the specific alternative antivirulent treatments for severe diseases caused by S. aureus can potentially settle a number of problems and difficulties of post-antibiotic era.

scholarly journals The Lipid Virulence Factors of Mycobacterium tuberculosis Exert Multilayered Control over Autophagy-Related Pathways in Infected Human Macrophages

Cells ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 666 ◽  
Author(s):  
Aïcha Bah ◽  
Merlin Sanicas ◽  
Jérôme Nigou ◽  
Christophe Guilhot ◽  
Catherine Astarie-Dequeker ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Virulence Factors ◽  
Defense Mechanism ◽  
Immune Defense ◽  
Knock Out ◽  
Human Macrophages ◽  
Type Vii Secretion ◽  
Type Vii Secretion System ◽  
Phagosomal Membrane ◽  
Phthiocerol Dimycocerosates

Autophagy is an important innate immune defense mechanism that controls Mycobacterium tuberculosis (Mtb) growth inside macrophages. Autophagy machinery targets Mtb-containing phagosomes via xenophagy after damage to the phagosomal membrane due to the Type VII secretion system Esx-1 or via LC3-associated phagocytosis without phagosomal damage. Conversely, Mtb restricts autophagy-related pathways via the production of various bacterial protein factors. Although bacterial lipids are known to play strategic functions in Mtb pathogenesis, their role in autophagy manipulation remains largely unexplored. Here, we report that the lipid virulence factors sulfoglycolipids (SLs) and phthiocerol dimycocerosates (DIMs) control autophagy-related pathways through distinct mechanisms in human macrophages. Using knock-out and knock-in mutants of Mtb and Mycobacterium bovis BCG (Bacille Calmette Guerin) and purified lipids, we found that (i) Mtb mutants with DIM and SL deficiencies promoted functional autophagy via an MyD88-dependent and phagosomal damage-independent pathway in human macrophages; (ii) SLs limited this pathway by acting as TLR2 antagonists; (iii) DIMs prevented phagosomal damage-independent autophagy while promoting Esx-1-dependent xenophagy; (iv) and DIMs, but not SLs, limited the acidification of LC3-positive Mtb compartments. In total, our study reveals an unexpected and intricate role for Mtb lipid virulence factors in controlling autophagy-related pathways in human macrophages, thus providing further insight into the autophagy manipulation tactics deployed by intracellular bacterial pathogens.

scholarly journals Hierarchical management of carbon sources is regulated similarly by the CbrA/B systems in Pseudomonas aeruginosa and Pseudomonas putida

Microbiology ◽  
2014 ◽  
Vol 160 (10) ◽  
pp. 2243-2252 ◽  
Author(s):  
Martina Valentini ◽  
Sofía M. García-Mauriño ◽  
Isabel Pérez-Martínez ◽  
Eduardo Santero ◽  
Inés Canosa ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Pseudomonas Putida ◽  
Nitrogen Availability ◽  
Carbon Sources ◽  
Signal Transduction Pathway ◽  
Exact Nature ◽  
Energy Status ◽  
Regulatory Systems ◽  
Close Relationship ◽  
Carbon Nitrogen Ratio

The CbrA/B system in pseudomonads is involved in the utilization of carbon sources and carbon catabolite repression (CCR) through the activation of the small RNAs crcZ in Pseudomonas aeruginosa, and crcZ and crcY in Pseudomonas putida. Interestingly, previous works reported that the CbrA/B system activity in P. aeruginosa PAO1 and P. putida KT2442 responded differently to the presence of different carbon sources, thus raising the question of the exact nature of the signal(s) detected by CbrA. Here, we demonstrated that the CbrA/B/CrcZ(Y) signal transduction pathway is similarly activated in the two Pseudomonas species. We show that the CbrA sensor kinase is fully interchangeable between the two species and, moreover, responds similarly to the presence of different carbon sources. In addition, a metabolomics analysis supported the hypothesis that CCR responds to the internal energy status of the cell, as the internal carbon/nitrogen ratio seems to determine CCR and non-CCR conditions. The strong difference found in the 2-oxoglutarate/glutamine ratio between CCR and non-CCR conditions points to the close relationship between carbon and nitrogen availability, or the relationship between the CbrA/B and NtrB/C systems, suggesting that both regulatory systems sense the same sort or interrelated signal.

scholarly journals Pathogenic Biohacking: Induction, Modulation and Subversion of Host Transcriptional Responses by Listeria monocytogenes

Toxins ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 294
Author(s):  
Matthew J. G. Eldridge ◽  
Pascale Cossart ◽  
Mélanie A. Hamon
Keyword(s):  
Gene Expression ◽  
Listeria Monocytogenes ◽  
Virulence Factors ◽  
Bacterial Pathogen ◽  
Typical Feature ◽  
Host Gene ◽  
Host Cells ◽  
Host Gene Expression ◽  
Transcriptional Responses ◽  
The Impact

During infection, the foodborne bacterial pathogen Listeria monocytogenes dynamically influences the gene expression profile of host cells. Infection-induced transcriptional changes are a typical feature of the host-response to bacteria and contribute to the activation of protective genes such as inflammatory cytokines. However, by using specialized virulence factors, bacterial pathogens can target signaling pathways, transcription factors, and epigenetic mechanisms to alter host gene expression, thereby reprogramming the response to infection. Therefore, the transcriptional profile that is established in the host is delicately balanced between antibacterial responses and pathogenesis, where any change in host gene expression might significantly influence the outcome of infection. In this review, we discuss the known transcriptional and epigenetic processes that are engaged during Listeria monocytogenes infection, the virulence factors that can remodel them, and the impact these processes have on the outcome of infection.

scholarly journals Inactivation of Phospholipase D Diminishes Acinetobacter baumannii Pathogenesis

2010 ◽  
Vol 78 (5) ◽  
pp. 1952-1962 ◽  
Author(s):  
Anna C. Jacobs ◽  
Indriati Hood ◽  
Kelli L. Boyd ◽  
Patrick D. Olson ◽  
John M. Morrison ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Virulence Factors ◽  
Phospholipase D ◽  
Cell Invasion ◽  
Regulatory Networks ◽  
Bacterial Pathogen ◽  
Ventilator Associated Pneumonia ◽  
Mutant Library ◽  
Strain Background ◽  
Epithelial Cell Invasion

ABSTRACT Acinetobacter baumannii is an emerging bacterial pathogen of considerable health care concern. Nonetheless, relatively little is known about the organism's virulence factors or their regulatory networks. Septicemia and ventilator-associated pneumonia are two of the more severe forms of A. baumannii disease. To identify virulence factors that may contribute to these disease processes, genetically diverse A. baumannii clinical isolates were evaluated for the ability to proliferate in human serum. A transposon mutant library was created in a strain background that propagated well in serum and screened for members with decreased serum growth. The results revealed that disruption of A. baumannii phospholipase D (PLD) caused a reduction in the organism's ability to thrive in serum, a deficiency in epithelial cell invasion, and diminished pathogenesis in a murine model of pneumonia. Collectively, these results suggest that PLD is an A. baumannii virulence factor.

scholarly journals miR-190, CDK1, MCM10 and NDC80 predict the prognosis of the patients with lung cancer

2019 ◽  
Vol 27 (1) ◽  
pp. 15-24
Author(s):  
Li-Wei Gao ◽  
Guo-Liang Wang
Keyword(s):  
Lung Cancer ◽  
Lung Carcinoma ◽  
Small Cell Lung Carcinoma ◽  
Small Cell ◽  
Normal Lung ◽  
Ppi Network ◽  
Small Cell Lung ◽  
Cell Lung Carcinoma ◽  
Network Modules ◽  
Tcga Dataset

Abstract Lung cancer (LC), which includes small-cell lung carcinoma (SCLC) and non-small-cell lung carcinoma (NSCLC), is common and has a high fatality rate. This study aimed to reveal the prognostic mechanisms of LC. GSE30219 was extracted from the Gene Expression Omnibus (GEO) database, and included 293 LC samples and 14 normal lung samples. Differentially expressed genes (DEGs) were identified using the Limma package, and subjected to pathway enrichment analysis using DAVID. MicroRNAs (miRNAs) targeting the DEGs were predicted using Webgestalt. Cytoscape software was used to build a protein-protein interaction (PPI) network and to identify significant network modules. Survival analysis was conducted using Survminer and Survival packages, and validation was performed using The Cancer Genome Atlas (TCGA) dataset. The good and poor prognosis groups contained 518 DEGs. miR-190, miR-493, and miR-218 for the upregulated genes and miR-302, miR-200, and miR-26 for the downregulated genes were predicted. Three network modules (module 1, 2, and 3) were identified from the PPI network. CDK1, MCM10, and NDC80 were the core nodes of module 1, 2, and 3, respectively. In module 1, CDK1 interacted with both CCNB1 and CCNB2. Additionally, CDK1, CCNB1, CCNB2, MCM10, and NDC80 expression levels correlated with clinical survival and were identified as DEGs in both GSE30219 and the TCGA dataset. miR-190, miR-493, miR-218, miR-200, and miR-302 might act in LC by targeting the DEGs. CDK1, CCNB1, CCNB2, MCM10, and NDC80 might also influence the prognosis of LC.

scholarly journals Review of phosphocholine substituents on bacterial pathogen glycans: Synthesis, structures and interactions with host proteins

2021 ◽  
Author(s):  
Warren W. Wakarchuk
Keyword(s):  
Immune System ◽  
Bacterial Pathogen ◽  
Adaptive Immune System ◽  
Infection Process ◽  
Innate Immune ◽  
Host Proteins ◽  
Adaptive Immune ◽  
Carbohydrate Components ◽  
Multiple Interactions ◽  
Structural Aspects

Among the non-carbohydrate components of glycans, the addition of phosphocholine (ChoP) to the glycans of pathogens occurs more rarely than acetylation or methylation, but it has far more potent biological consequences. These arise from ChoP's multiple interactions with host proteins, which are important at all stages of the infection process. These stages include initial adherence to cells, encountering the host's innate immune system and then the adaptive immune system. Thus, in the initial stages of an infection, ChoP groups are an asset to the pathogen, but they can turn into a disadvantage subsequently. In this review, we have focussed on structural aspects of these phenomena. We describe the biosynthesis of the ChoP modification, the structures of the pathogen glycans known to carry ChoP groups and the host proteins that recognize ChoP.

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