scholarly journals Yin and Yang of Biofilm Formation and Cyclic di-GMP Signaling of the Gastrointestinal Pathogen Salmonella enterica Serovar Typhimurium

2021 ◽  
pp. 1-18
Author(s):  
Agaristi Lamprokostopoulou ◽  
Ute Römling
Keyword(s):  
Biofilm Formation ◽  
Second Messenger ◽  
Bacterial Biofilm ◽  
Chronic Infections ◽  
Nutrient Sources ◽  
Microbial Biofilms ◽  
Extracellular Signaling ◽  
Serovar Typhimurium ◽  
Yin And Yang ◽  
Second Messenger Signaling

Within the last 60 years, microbiological research has challenged many dogmas such as bacteria being unicellular microorganisms directed by nutrient sources; these investigations produced new dogmas such as cyclic diguanylate monophosphate (cyclic di-GMP) second messenger signaling as a ubiquitous regulator of the fundamental sessility/motility lifestyle switch on the single-cell level. Successive investigations have not yet challenged this view; however, the complexity of cyclic di-GMP as an intracellular bacterial signal, and, less explored, as an extracellular signaling molecule in combination with the conformational flexibility of the molecule, provides endless opportunities for cross-kingdom interactions. Cyclic di-GMP-directed microbial biofilms commonly stimulate the immune system on a lower level, whereas host-sensed cyclic di-GMP broadly stimulates the innate and adaptive immune responses. Furthermore, while the intracellular second messenger cyclic di-GMP signaling promotes bacterial biofilm formation and chronic infections, oppositely, <i>Salmonella</i> Typhimurium cellulose biofilm inside immune cells is not endorsed. These observations only touch on the complexity of the interaction of biofilm microbial cells with its host. In this review, we describe the Yin and Yang interactive concepts of biofilm formation and cyclic di-GMP signaling using <i>S</i>. Typhimurium as an example.

scholarly journals Inhibition of Salmonella enterica Biofilm Formation Using Small-Molecule Adenosine Mimetics

2014 ◽  
Vol 59 (1) ◽  
pp. 76-84 ◽  
Author(s):  
Jacob A. Koopman ◽  
Joanna M. Marshall ◽  
Aditi Bhatiya ◽  
Tadesse Eguale ◽  
Jesse J. Kwiek ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Biofilm Formation ◽  
Mammalian Cells ◽  
Bacterial Species ◽  
Binding Pocket ◽  
Bacterial Biofilm ◽  
Chronic Infections ◽  
Content Type ◽  
Cellular Processes ◽  
Serovar Typhimurium

ABSTRACTBiofilms have been widely implicated in chronic infections and environmental persistence ofSalmonella enterica, facilitating enhanced colonization of surfaces and increasing the ability of the bacteria to be transmitted to new hosts.Salmonella entericaserovar Typhi biofilm formation on gallstones from humans and mice enhances gallbladder colonization and bacterial shedding, whileSalmonella entericaserovar Typhimurium biofilms facilitate long-term persistence in a number of environments important to food, medical, and farming industries.Salmonellaregulates expression of many virulence- and biofilm-related processes using kinase-driven pathways. Kinases play pivotal roles in phosphorylation and energy transfer in cellular processes and possess an ATP-binding pocket required for their functions. Many other cellular proteins also require ATP for their activity. Here we test the hypothesis that pharmacological interference with ATP-requiring enzymes utilizing adenosine mimetic compounds would decrease or inhibit bacterial biofilm formation. Through the screening of a 3,000-member ATP mimetic library, we identified a single compound (compound 7955004) capable of significantly reducing biofilm formation byS. Typhimurium andS. Typhi. The compound was not bactericidal or bacteriostatic towardS. Typhimurium or cytotoxic to mammalian cells. An ATP-Sepharose affinity matrix technique was used to discover potential protein-binding targets of the compound and identified GroEL and DeoD. Compound 7955004 was screened against other known biofilm-forming bacterial species and was found to potently inhibit biofilms ofAcinetobacter baumanniias well. The identification of a lead compound with biofilm-inhibiting capabilities towardSalmonellaprovides a potential new avenue of therapeutic intervention againstSalmonellabiofilm formation, with applicability to biofilms of other bacterial pathogens.

scholarly journals More than Enzymes That Make or Break Cyclic Di-GMP—Local Signaling in the Interactome of GGDEF/EAL Domain Proteins of Escherichia coli

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
Author(s):  
Olga Sarenko ◽  
Gisela Klauck ◽  
Franziska M. Wilke ◽  
Vanessa Pfiffer ◽  
Anja M. Richter ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Biofilm Formation ◽  
Second Messenger ◽  
Bacterial Biofilm ◽  
Interaction Patterns ◽  
Systematic Analysis ◽  
E Coli ◽  
Diguanylate Cyclases ◽  
Hub Proteins ◽  
Effector Target

ABSTRACT The bacterial second messenger bis-(3′-5′)-cyclic diguanosine monophosphate (c-di-GMP) ubiquitously promotes bacterial biofilm formation. Intracellular pools of c-di-GMP seem to be dynamically negotiated by diguanylate cyclases (DGCs, with GGDEF domains) and specific phosphodiesterases (PDEs, with EAL or HD-GYP domains). Most bacterial species possess multiple DGCs and PDEs, often with surprisingly distinct and specific output functions. One explanation for such specificity is “local” c-di-GMP signaling, which is believed to involve direct interactions between specific DGC/PDE pairs and c-di-GMP-binding effector/target systems. Here we present a systematic analysis of direct protein interactions among all 29 GGDEF/EAL domain proteins of Escherichia coli . Since the effects of interactions depend on coexpression and stoichiometries, cellular levels of all GGDEF/EAL domain proteins were also quantified and found to vary dynamically along the growth cycle. Instead of detecting specific pairs of interacting DGCs and PDEs, we discovered a tightly interconnected protein network of a specific subset or “supermodule” of DGCs and PDEs with a coregulated core of five hyperconnected hub proteins. These include the DGC/PDE proteins representing the c-di-GMP switch that turns on biofilm matrix production in E. coli . Mutants lacking these core hub proteins show drastic biofilm-related phenotypes but no changes in cellular c-di-GMP levels. Overall, our results provide the basis for a novel model of local c-di-GMP signaling in which a single strongly expressed master PDE, PdeH, dynamically eradicates global effects of several DGCs by strongly draining the global c-di-GMP pool and thereby restricting these DGCs to serving as local c-di-GMP sources that activate specific colocalized effector/target systems. IMPORTANCE c-di-GMP signaling in bacteria is believed to occur via changes in cellular c-di-GMP levels controlled by antagonistic and potentially interacting pairs of diguanylate cyclases (DGCs) and c-di-GMP phosphodiesterases (PDEs). Our systematic analysis of protein-protein interaction patterns of all 29 GGDEF/EAL domain proteins of E. coli , together with our measurements of cellular c-di-GMP levels, challenges both aspects of this current concept. Knocking out distinct DGCs and PDEs has drastic effects on E. coli biofilm formation without changing the cellular c-di-GMP level. In addition, rather than generally coming in interacting DGC/PDE pairs, a subset of DGCs and PDEs operates as central interaction hubs in a larger "supermodule," with other DGCs and PDEs behaving as “lonely players” without contacts to other c-di-GMP-related enzymes. On the basis of these data, we propose a novel concept of “local” c-di-GMP signaling in bacteria with multiple enzymes that make or break the second messenger c-di-GMP.

scholarly journals Bacterial Biofilm Growth on 3D-Printed Materials

2021 ◽  
Vol 12 ◽  
Author(s):  
Donald C. Hall ◽  
Phillip Palmer ◽  
Hai-Feng Ji ◽  
Garth D. Ehrlich ◽  
Jarosław E. Król
Keyword(s):  
Medical Devices ◽  
Biofilm Formation ◽  
Antimicrobial Agents ◽  
Bacterial Attachment ◽  
Bacterial Biofilm ◽  
Chronic Infections ◽  
Biofilm Growth ◽  
Wide Range ◽  
3D Printed ◽  
Printed Materials

Recent advances in 3D printing have led to a rise in the use of 3D printed materials in prosthetics and external medical devices. These devices, while inexpensive, have not been adequately studied for their ability to resist biofouling and biofilm buildup. Bacterial biofilms are a major cause of biofouling in the medical field and, therefore, hospital-acquired, and medical device infections. These surface-attached bacteria are highly recalcitrant to conventional antimicrobial agents and result in chronic infections. During the COVID-19 pandemic, the U.S. Food and Drug Administration and medical officials have considered 3D printed medical devices as alternatives to conventional devices, due to manufacturing shortages. This abundant use of 3D printed devices in the medical fields warrants studies to assess the ability of different microorganisms to attach and colonize to such surfaces. In this study, we describe methods to determine bacterial biofouling and biofilm formation on 3D printed materials. We explored the biofilm-forming ability of multiple opportunistic pathogens commonly found on the human body including Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus to colonize eight commonly used polylactic acid (PLA) polymers. Biofilm quantification, surface topography, digital optical microscopy, and 3D projections were employed to better understand the bacterial attachment to 3D printed surfaces. We found that biofilm formation depends on surface structure, hydrophobicity, and that there was a wide range of antimicrobial properties among the tested polymers. We compared our tested materials with commercially available antimicrobial PLA polymers.

scholarly journals A Conserved Regulatory Circuit Controls Large Adhesins in Vibrio cholerae

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
Giordan Kitts ◽  
Krista M. Giglio ◽  
David Zamorano-Sánchez ◽  
Jin Hwan Park ◽  
Loni Townsley ◽  
...  
Keyword(s):  
Cell Surface ◽  
Vibrio Cholerae ◽  
Biofilm Formation ◽  
Diarrheal Disease ◽  
Cell Attachment ◽  
Surface Display ◽  
Second Messenger ◽  
Bacterial Biofilm ◽  
Content Type ◽  
Regulatory Circuit

ABSTRACT The dinucleotide second messenger c-di-GMP has emerged as a central regulator of reversible cell attachment during bacterial biofilm formation. A prominent cell adhesion mechanism first identified in pseudomonads combines two c-di-GMP-mediated processes: transcription of a large adhesin and its cell surface display via posttranslational proteolytic control. Here, we characterize an orthologous c-di-GMP effector system and show that it is operational in Vibrio cholerae, where it regulates two distinct classes of adhesins. Through structural analyses, we reveal a conserved autoinhibition mechanism of the c-di-GMP receptor that controls adhesin proteolysis and present a structure of a c-di-GMP-bound receptor module. We further establish functionality of the periplasmic protease controlled by the receptor against the two adhesins. Finally, transcription and functional assays identify physiological roles of both c-di-GMP-regulated adhesins in surface attachment and biofilm formation. Together, our studies highlight the conservation of a highly efficient signaling effector circuit for the control of cell surface adhesin expression and its versatility by revealing strain-specific variations. IMPORTANCE Vibrio cholerae, the causative agent of the diarrheal disease cholera, benefits from a sessile biofilm lifestyle that enhances survival outside the host but also contributes to host colonization and infectivity. The bacterial second messenger c-di-GMP has been identified as a central regulator of biofilm formation, including in V. cholerae; however, our understanding of the pathways that contribute to this process is incomplete. Here, we define a conserved signaling system that controls the stability of large adhesion proteins at the cell surface of V. cholerae, which are important for cell attachment and biofilm formation. Insight into the regulatory circuit underlying biofilm formation may inform targeted strategies to interfere with a process that renders this bacterium remarkably adaptable to changing environments.

scholarly journals In SilicoDiscovery andIn VitroValidation of Catechol-Containing Sulfonohydrazide Compounds as Potent Inhibitors of the Diguanylate Cyclase PleD

2015 ◽  
Vol 198 (1) ◽  
pp. 147-156 ◽  
Author(s):  
Silvia Fernicola ◽  
Alessandro Paiardini ◽  
Giorgio Giardina ◽  
Giordano Rampioni ◽  
Livia Leoni ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Pathogenic Bacteria ◽  
Caulobacter Crescentus ◽  
Pharmacophore Model ◽  
Second Messenger ◽  
Binding Mode ◽  
Structural Features ◽  
Bacterial Biofilm ◽  
Content Type

ABSTRACTBiofilm formation is responsible for increased antibiotic tolerance in pathogenic bacteria. Cyclic di-GMP (c-di-GMP) is a widely used second-messenger signal that plays a key role in bacterial biofilm formation. c-di-GMP is synthesized by diguanylate cyclases (DGCs), a conserved class of enzymes absent in mammals and hence considered attractive molecular targets for the development of antibiofilm agents. Here, the results of a virtual screening approach aimed at identifying small-molecule inhibitors of the DGC PleD fromCaulobacter crescentusare described. A three-dimensional (3D) pharmacophore model, derived from the mode of binding of GTP to the active site of PleD, was exploited to screen the ZINC database of compounds. Seven virtual hits were testedin vitrofor their ability to inhibit the activity of purified PleD by using circular dichroism spectroscopy. Two drug-like molecules with a catechol moiety and a sulfonohydrazide scaffold were shown to competitively inhibit PleD at the low-micromolar range (50% inhibitory concentration [IC50] of ∼11 μM). Their predicted binding mode highlighted key structural features presumably responsible for the efficient inhibition of PleD by both hits. These molecules represent the most potentin vitroinhibitors of PleD identified so far and could therefore result in useful leads for the development of novel classes of antimicrobials able to hamper biofilm formation.IMPORTANCEBiofilm-mediated infections are difficult to eradicate, posing a threatening health issue worldwide. The capability of bacteria to form biofilms is almost universally stimulated by the second messenger c-di-GMP. This evidence has boosted research in the last decade for the development of new antibiofilm strategies interfering with c-di-GMP metabolism. Here, two potent inhibitors of c-di-GMP synthesis have been identifiedin silicoand characterizedin vitroby using the well-characterized DGC enzyme PleD fromC. crescentusas a structural template and molecular target. Given that the protein residues implied as crucial for enzyme inhibition are found to be highly conserved among DGCs, the outcome of this study could pave the way for the future development of broad-spectrum antibiofilm compounds.

scholarly journals The Role of Bacterial Biofilm in Antibiotic Resistance and Food Contamination

2020 ◽  
Vol 2020 ◽  
pp. 1-10 ◽  
Author(s):  
Gedif Meseret Abebe
Keyword(s):  
Antibiotic Resistance ◽  
Food Processing ◽  
Biofilm Formation ◽  
Extracellular Polymeric Substances ◽  
Food Contamination ◽  
Bacterial Biofilm ◽  
Natural Environments ◽  
Chronic Infections ◽  
Related Factors

Biofilm is a microbial association or community attached to different biotic or abiotic surfaces or environments. These surface-attached microbial communities can be found in food, medical, industrial, and natural environments. Biofilm is a critical problem in the medical sector since it is formed on medical implants within human tissue and involved in a multitude of serious chronic infections. Food and food processing surface become an ideal environment for biofilm formation where there are sufficient nutrients for microbial growth and attachment. Therefore, biofilm formation on these surfaces, especially on food processing surface becomes a challenge in food safety and human health. Microorganisms within a biofilm are encased within a matrix of extracellular polymeric substances that can act as a barrier and recalcitrant for different hostile conditions such as sanitizers, antibiotics, and other hygienic conditions. Generally, they persist and exist in food processing environments where they become a source of cross-contamination and foodborne diseases. The other critical issue with biofilm formation is their antibiotic resistance which makes medication difficult, and they use different physical, physiological, and gene-related factors to develop their resistance mechanisms. In order to mitigate their production and develop controlling methods, it is better to understand growth requirements and mechanisms. Therefore, the aim of this review article is to provide an overview of the role of bacterial biofilms in antibiotic resistance and food contamination and emphasizes ways for controlling its production.

scholarly journals Intercepting second-messenger signaling by rationally designed peptides sequestering c-di-GMP

2020 ◽  
Vol 117 (29) ◽  
pp. 17211-17220 ◽  
Author(s):  
Chee-Seng Hee ◽  
Judith Habazettl ◽  
Christoph Schmutz ◽  
Tilman Schirmer ◽  
Urs Jenal ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Complex Structure ◽  
Second Messenger ◽  
Effector Protein ◽  
Binding Motif ◽  
Stacking Interactions ◽  
Cellular Functions ◽  
Growth And Survival ◽  
Wide Range ◽  
Second Messenger Signaling

The bacterial second messenger cyclic diguanylate (c-di-GMP) regulates a wide range of cellular functions from biofilm formation to growth and survival. Targeting a second-messenger network is challenging because the system involves a multitude of components with often overlapping functions. Here, we present a strategy to intercept c-di-GMP signaling pathways by directly targeting the second messenger. For this, we developed a c-di-GMP–sequestering peptide (CSP) that was derived from a CheY-like c-di-GMP effector protein. CSP binds c-di-GMP with submicromolar affinity. The elucidation of the CSP⋅c-di-GMP complex structure by NMR identified a linear c-di-GMP–binding motif, in which a self-intercalated c-di-GMP dimer is tightly bound by a network of H bonds and π-stacking interactions involving arginine and aromatic residues. Structure-based mutagenesis yielded a variant with considerably higher, low-nanomolar affinity, which subsequently was shortened to 19 residues with almost uncompromised affinity. We demonstrate that endogenously expressed CSP intercepts c-di-GMP signaling and effectively inhibits biofilm formation inPseudomonas aeruginosa, the most widely used model for serious biofilm-associated medical implications.

scholarly journals Identification of Small Molecules That Antagonize Diguanylate Cyclase Enzymes To Inhibit Biofilm Formation

2012 ◽  
Vol 56 (10) ◽  
pp. 5202-5211 ◽  
Author(s):  
Karthik Sambanthamoorthy ◽  
Rudolph E. Sloup ◽  
Vijay Parashar ◽  
Joshua M. Smith ◽  
Eric E. Kim ◽  
...  
Keyword(s):  
Small Molecules ◽  
Biofilm Formation ◽  
Flow System ◽  
Total Concentration ◽  
Bacterial Biofilm ◽  
Diguanylate Cyclase ◽  
Signaling System ◽  
Chronic Infections ◽  
Content Type ◽  
New Strategies

ABSTRACTBacterial biofilm formation is responsible for numerous chronic infections, causing a severe health burden. Many of these infections cannot be resolved, as bacteria in biofilms are resistant to the host's immune defenses and antibiotic therapy. New strategies to treat biofilm-based infections are critically needed. Cyclic di-GMP (c-di-GMP) is a widely conserved second-messenger signal essential for biofilm formation. As this signaling system is found only in bacteria, it is an attractive target for the development of new antibiofilm interventions. Here, we describe the results of a high-throughput screen to identify small-molecule inhibitors of diguanylate cyclase (DGC) enzymes that synthesize c-di-GMP. We report seven small molecules that antagonize these enzymes and inhibit biofilm formation byVibrio cholerae. Moreover, two of these compounds significantly reduce the total concentration of c-di-GMP inV. cholerae, one of which also inhibits biofilm formation byPseudomonas aeruginosain a continuous-flow system. These molecules represent the first compounds described that are able to inhibit DGC activity to prevent biofilm formation.

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