scholarly journals Agent-Based Modeling Demonstrates How Local Chemotactic Behavior Can Shape Biofilm Architecture

2018 ◽  
Author(s):  
Emily G. Sweeney ◽  
Andrew Nishida ◽  
Alexandra Weston ◽  
Maria S. Bañuelos ◽  
Kristin Potter ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Three Dimensional ◽  
Structural Features ◽  
Agent Based Modeling ◽  
Emergent Properties ◽  
Cellular Interactions ◽  
Biofilm Growth ◽  
Agent Based ◽  
Autoinducer 2 ◽  
H Pylori

AbstractMature bacterial biofilms have elaborate three-dimensional architectures that endow these structures with their durability and resistance to environmental perturbations. We used agent-based modeling to explore whether local cellular interactions were sufficient to give rise to global structural features of biofilms. Specifically, we asked whether chemorepulsion from a self-produced quorum-sensing molecule, autoinducer-2 (AI-2), was sufficient to recapitulate biofilm growth and cellular organization observed for biofilms of the human pathogen Helicobacter pylori. To carry out this modeling, we modified an existing platform, Individual-based Dynamics of Microbial Communities Simulator (iDynoMiCS), to incorporate three-dimensional chemotaxis, planktonic cells that could join or leave the biofilm structure, and cellular production of AI-2. We simulated biofilm growth of previously characterized H. pylori strains with varying AI-2 production and sensing capacities. Using biologically plausible parameters, we were able to recapitulate both the variation in biofilm mass and cellular distributions observed with these strains. Specifically, the strains that were competent to chemotax away from AI-2 produced smaller and more heterogeneously spaced biofilms, whereas the AI-2 chemotaxis defective strains produced larger and more homogeneously spaced biofilms. The model also provided new insights into the cellular demographics contributing to the biofilm patterning of each strain. Our analysis supports the idea that cellular interactions at small spatial and temporal scales are sufficient to give rise to larger scale emergent properties of biofilms.ImportanceMost bacteria exist in aggregated, three-dimensional structures called biofilms. Biofilms are resistant to antimicrobials and can pose societal problems, for example when they grow in plumbing systems or on medical implants. Understanding the processes that promote the growth and disassembly of biofilms could lead to better strategies to manage these structures. We had previously shown that Helicobacter pylori bacteria are repulsed by high concentrations of a self-produced molecule, autoinducer-2 (AI-2) and that H. pylori mutants deficient in AI-2 sensing form larger and more homogeneously spaced biofilms. Here we used computer simulations of biofilm formation to show that local H. pylori behavior of repulsion from high AI-2 could explain the overall architecture of H. pylori biofilms. Our findings demonstrate that it is possible to change global biofilm organization by manipulating local cell behaviors, which suggests that simple strategies targeting cells at local scales could be useful for controlling biofilms in industrial and medical settings.

scholarly journals Agent-Based Modeling Demonstrates How Local Chemotactic Behavior Can Shape Biofilm Architecture

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Emily G. Sweeney ◽  
Andrew Nishida ◽  
Alexandra Weston ◽  
Maria S. Bañuelos ◽  
Kristin Potter ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Three Dimensional ◽  
Structural Features ◽  
Agent Based Modeling ◽  
Emergent Properties ◽  
Cellular Interactions ◽  
Biofilm Growth ◽  
Content Type ◽  
Agent Based ◽  
H Pylori

ABSTRACTBacteria are often found living in aggregated multicellular communities known as biofilms. Biofilms are three-dimensional structures that confer distinct physical and biological properties to the collective of cells living within them. We used agent-based modeling to explore whether local cellular interactions were sufficient to give rise to global structural features of biofilms. Specifically, we asked whether chemorepulsion from a self-produced quorum-sensing molecule, autoinducer-2 (AI-2), was sufficient to recapitulate biofilm growth and cellular organization observed for biofilms ofHelicobacter pylori, a common bacterial resident of human stomachs. To carry out this modeling, we modified an existing platform, Individual-based Dynamics of Microbial Communities Simulator (iDynoMiCS), to incorporate three-dimensional chemotaxis, planktonic cells that could join or leave the biofilm structure, and cellular production of AI-2. We simulated biofilm growth of previously characterizedH. pyloristrains with various AI-2 production and sensing capacities. Using biologically plausible parameters, we were able to recapitulate both the variation in biofilm mass and cellular distributions observed with these strains. Specifically, the strains that were competent to chemotax away from AI-2 produced smaller and more heterogeneously spaced biofilms, whereas the AI-2 chemotaxis-defective strains produced larger and more homogeneously spaced biofilms. The model also provided new insights into the cellular demographics contributing to the biofilm patterning of each strain. Our analysis supports the idea that cellular interactions at small spatial and temporal scales are sufficient to give rise to larger-scale emergent properties of biofilms.IMPORTANCEMost bacteria exist in aggregated, three-dimensional structures called biofilms. Although biofilms play important ecological roles in natural and engineered settings, they can also pose societal problems, for example, when they grow in plumbing systems or on medical implants. Understanding the processes that promote the growth and disassembly of biofilms could lead to better strategies to manage these structures. We had previously shown thatHelicobacter pyloribacteria are repulsed by high concentrations of a self-produced molecule, AI-2, and thatH. pylorimutants deficient in AI-2 sensing form larger and more homogeneously spaced biofilms. Here, we used computer simulations of biofilm formation to show that localH. pyloribehavior of repulsion from high AI-2 could explain the overall architecture ofH. pyloribiofilms. Our findings demonstrate that it is possible to change global biofilm organization by manipulating local cell behaviors, which suggests that simple strategies targeting cells at local scales could be useful for controlling biofilms in industrial and medical settings.

scholarly journals Chemorepulsion from the Quorum Signal Autoinducer-2 Promotes Helicobacter pylori Biofilm Dispersal

mBio ◽  
2015 ◽  
Vol 6 (4) ◽  
Author(s):  
Jeneva K. Anderson ◽  
Julie Y. Huang ◽  
Christopher Wreden ◽  
Emily Goers Sweeney ◽  
John Goers ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Quorum Sensing ◽  
Spatial Organization ◽  
Adherent Cells ◽  
Dependent Manner ◽  
Biofilm Growth ◽  
Content Type ◽  
Autoinducer 2 ◽  
Periplasmic Binding Proteins ◽  
H Pylori

ABSTRACT The gastric pathogen Helicobacter pylori forms biofilms on abiotic and biotic surfaces. We have shown previously that H. pylori perceives the quorum signal autoinducer-2 (AI-2) as a chemorepellent. We report here that H. pylori chemorepulsion from endogenous AI-2 influences the proportions and spatial organization of cells within biofilms. Strains that fail to produce AI-2 (∆luxS strains) or are defective for chemotaxis (∆cheA strains) formed more spatially homogenous biofilms with a greater proportion of adherent versus planktonic cells than wild-type biofilms. Reciprocally, a strain that overproduced AI-2 (luxSOP ) formed biofilms with proportionally fewer adherent cells. Along with the known AI-2 chemoreceptor, TlpB, we identified AibA and AibB, two novel periplasmic binding proteins that are required for the AI-2 chemorepulsion response. Disruptions in any of the proteins required for AI-2 chemotaxis recapitulated the biofilm adherence and spatial organization phenotype of the ∆luxS mutant. Furthermore, exogenous administration of AI-2 was sufficient to decrease the proportion of adherent cells in biofilms and promote dispersal of cells from biofilms in a chemotaxis-dependent manner. Finally, we found that disruption of AI-2 production or AI-2 chemotaxis resulted in increased clustering of cells in microcolonies on cultured epithelial cells. We conclude that chemotaxis from AI-2 is a determinant of H. pylori biofilm spatial organization and dispersal. IMPORTANCE Bacterial biofilms are ubiquitous in nature, but the mechanisms governing their assembly and spatial organization are not fully understood. Bacterial communication through quorum sensing has been shown to influence biofilm growth through the regulation of biofilm genes. Our study revealed a new role for quorum sensing in biofilms through rapid chemotactic responses to quorum signals. Specifically, we studied how chemorepulsion of Helicobacter pylori from the universal quorum signal autoinducer-2 (AI-2) shapes the spatial organization of its biofilms. We demonstrate that the chemorepulsive response of H. pylori to AI-2 is necessary to promote its dispersal from biofilms grown on both abiotic and biotic surfaces and is sufficient to promote dispersal in a chemotaxis-dependent manner. This work has broad implications for understanding the mechanisms by which endogenously produced microbial compounds shape the assembly and spatial organization of microbial communities in their environments.

scholarly journals Growth Phase Regulation of flaA Expression in Helicobacter pylori Is luxS Dependent

2004 ◽  
Vol 72 (9) ◽  
pp. 5506-5510 ◽  
Author(s):  
John T. Loh ◽  
Mark H. Forsyth ◽  
Timothy L. Cover
Keyword(s):  
Helicobacter Pylori ◽  
Growth Phase ◽  
Wild Type ◽  
Phase Dependence ◽  
Autoinducer 2 ◽  
Extracellular Signaling ◽  
Reporter Strains ◽  
Phase Regulation ◽  
H Pylori

ABSTRACT LuxS plays a role in the synthesis of an extracellular signaling molecule, autoinducer 2 (AI-2). To analyze a possible role of AI-2 in regulating Helicobacter pylori gene expression, we constructed a panel of transcriptional reporter strains. We show that the expression of H. pylori flaA is growth phase dependent and that flaA transcription increases in association with increased culture density. Mutating the luxS gene eliminates growth-phase-dependent control of flaA, and this growth phase dependence is restored when the luxS mutant strain is complemented with the wild-type luxS gene.

scholarly journals Quantitative Effect of luxS Gene Inactivation on the Fitness of Helicobacter pylori

2006 ◽  
Vol 72 (10) ◽  
pp. 6615-6622 ◽  
Author(s):  
Woo-Kon Lee ◽  
Keiji Ogura ◽  
John T. Loh ◽  
Timothy L. Cover ◽  
Douglas E. Berg
Keyword(s):  
Helicobacter Pylori ◽  
Competitive Ability ◽  
Reference Strain ◽  
Bacterial Species ◽  
Soft Agar ◽  
Autoinducer 2 ◽  
Methyl Cycle ◽  
Adenosyl Methionine ◽  
Unrelated Strain ◽  
H Pylori

ABSTRACT Furanone metabolites called AI-2 (autoinducer 2), used by some bacterial species for signaling and cell density-regulated changes in gene expression, are made while regenerating S-adenosyl methionine (SAM) after its use as a methyl donor. The luxS-encoded enzyme, in particular, participates in this activated methyl cycle by generating both a pentanedione, which is transformed chemically into these AI-2 compounds, and homocysteine, a precursor of methionine and SAM. Helicobacter pylori seems to contain the genes for this activated methyl cycle, including luxS, but not genes for AI-2 uptake and transcriptional regulation. Here we report that deletion of luxS in H. pylori reference strain SS1 diminished its competitive ability in mice and motility in soft agar, whereas no such effect was seen with an equivalent ΔluxS derivative of the unrelated strain X47. These different outcomes are consistent with H. pylori's considerable genetic diversity and are reminiscent of phenotypes seen after deletion of another nonessential metabolic gene, that encoding polyphosphate kinase 1. We suggest that synthesis of AI-2 by H. pylori may be an inadvertent consequence of metabolite flux in its activated methyl cycle and that impairment of this cycle and/or pathways affected by it, rather than loss of quorum sensing, is deleterious for some H. pylori strains. Also tenable is a model in which AI-2 affects other microbes in H. pylori's gastric ecosystem and thereby modulates the gastric environment in ways to which certain H. pylori strains are particularly sensitive.

scholarly journals Construction and Characterization of aHelicobacter pylori clpB Mutant and Role of the Gene in the Stress Response

1998 ◽  
Vol 180 (2) ◽  
pp. 426-429 ◽  
Author(s):  
Elaine Allan ◽  
Peter Mullany ◽  
Soad Tabaqchali
Keyword(s):  
Helicobacter Pylori ◽  
High Temperature ◽  
Stress Response ◽  
Structural Features ◽  
High Temperature Stress ◽  
Gene Encoding ◽  
Increased Sensitivity ◽  
H Pylori

ABSTRACT Antiserum raised against whole Helicobacter pyloricells identified a novel 94-kDa antigen. The nucleotide sequence of the gene encoding the 94-kDa antigen was determined, and analysis of the deduced amino acid sequence revealed structural features typical of the ClpB ATPase family of stress response proteins. An isogenic H. pylori clpB mutant showed increased sensitivity to high-temperature stress, indicating that the clpB gene product functions as a stress response protein in H. pylori.

scholarly journals Genetic requirements and transcriptomics of Helicobacter pylori biofilm formation on abiotic and biotic surfaces

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Skander Hathroubi ◽  
Shuai Hu ◽  
Karen M. Ottemann
Keyword(s):  
Helicobacter Pylori ◽  
Biofilm Formation ◽  
Tca Cycle ◽  
Harsh Environments ◽  
Laboratory Model ◽  
Secretion Systems ◽  
Biofilm Growth ◽  
Tca Cycle Enzymes ◽  
Growth Properties ◽  
H Pylori

AbstractBiofilm growth is a widespread mechanism that protects bacteria against harsh environments, antimicrobials, and immune responses. These types of conditions challenge chronic colonizers such as Helicobacter pylori but it is not fully understood how H. pylori biofilm growth is defined and its impact on H. pylori survival. To provide insights into H. pylori biofilm growth properties, we characterized biofilm formation on abiotic and biotic surfaces, identified genes required for biofilm formation, and defined the biofilm-associated gene expression of the laboratory model H. pylori strain G27. We report that H. pylori G27 forms biofilms with a high biomass and complex flagella-filled 3D structures on both plastic and gastric epithelial cells. Using a screen for biofilm-defective mutants and transcriptomics, we discovered that biofilm cells demonstrated lower transcripts for TCA cycle enzymes but higher ones for flagellar formation, two type four secretion systems, hydrogenase, and acetone metabolism. We confirmed that biofilm formation requires flagella, hydrogenase, and acetone metabolism on both abiotic and biotic surfaces. Altogether, these data suggest that H. pylori is capable of adjusting its phenotype when grown as biofilm, changing its metabolism, and re-shaping flagella, typically locomotion organelles, into adhesive structures.

scholarly journals Bystander Effects of Hypoxia-Activated Prodrugs: Agent-Based Modeling Using Three Dimensional Cell Cultures

2018 ◽  
Vol 9 ◽  
Author(s):  
Cho R. Hong ◽  
Gib Bogle ◽  
Jingli Wang ◽  
Kashyap Patel ◽  
Frederik B. Pruijn ◽  
...  
Keyword(s):  
Cell Cultures ◽  
Three Dimensional ◽  
Agent Based Modeling ◽  
Bystander Effects ◽  
Agent Based ◽  
Dimensional Cell

scholarly journals Identification of two new Helicobacter pylori surface proteins involved in attachment to epithelial cell lines

2005 ◽  
Vol 54 (5) ◽  
pp. 427-434 ◽  
Author(s):  
Sebastian Rubinsztein-Dunlop ◽  
Bruno Guy ◽  
Ling Lissolo ◽  
Hans Fischer
Keyword(s):  
Helicobacter Pylori ◽  
Epithelial Cell ◽  
Epithelial Cells ◽  
Cell Lines ◽  
Gastric Epithelium ◽  
Cellular Interactions ◽  
Bacterial Adhesins ◽  
Epithelial Cell Lines ◽  
H Pylori ◽  
Adhesive Proteins

Helicobacter pylori causes the development of gastritis, gastric ulcers and adenocarcinomas in humans. The establishment of infection is influenced by adherence to the gastric epithelium, and several bacterial adhesins and host cell receptors have been identified. H. pylori recognize the Lewisb receptor through the BabA adhesin but also readily adhere to epithelia in the absence of the Lewisb epitope, demonstrating the relevance of additional adhesive interactions. This study presents a novel method of identifying bacterial adhesins. Nickel beads were coated with H. pylori-derived, recombinantly expressed ORF proteins, and epithelial cells from the human stomach, intestine or urinary tract were allowed to adhere to those beads. The binding of epithelial cells to the protein-coated nickel beads was confirmed by electron microscopy or flow cytometry using antibodies directed towards the His-tags. Among the five ORFs tested, two new adhesive proteins (HP1188 and HP1430) were identified. Both were expressed on the surface of virulent H. pylori, with the HP1188 protein being most abundant. The purified HP1188 and HP1430 proteins bound more strongly to gastric than to other epithelial cell lines, suggesting that they may be involved in the colonization of the human gastric mucosa. In conclusion, this method facilitates the identification of ORFs of microbial origin involved in cellular interactions such as adherence.

scholarly journals Helicobacter pylori Expresses an Autolytic Enzyme: Gene Identification, Cloning, and Theoretical Protein Structure

2002 ◽  
Vol 184 (22) ◽  
pp. 6270-6279 ◽  
Author(s):  
Eleonora Marsich ◽  
Pierfrancesco Zuccato ◽  
Sonia Rizzi ◽  
Amedeo Vetere ◽  
Enrico Tonin ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Bacteriophage T4 ◽  
Three Dimensional ◽  
Gene Identification ◽  
Gram Negative Bacteria ◽  
Hypothetical Gene ◽  
Autolytic Enzyme ◽  
Genetic Features ◽  
H Pylori ◽  
High Degree

ABSTRACT Helicobacter pylori is an important pathogen of the gastric system. The clinical outcome of infection is thought to be correlated with some genetic features of the bacterium. However, due to the extreme genetic variability of this organism, it is hard to draw definitive conclusions concerning its virulence factors. Here we describe a novel H. pylori gene which expresses an autolytic enzyme that is also capable of degrading the cell walls of both gram-positive and gram-negative bacteria. We designated this gene lys. We found this gene and observed its expression in a number of unrelated clinical strains, a fact that suggests that it is well conserved in the species. A comparison of the nucleotide sequences of lys and the hypothetical gene HP0339 from H. pylori strain ATCC 26695 revealed almost total identity, except for the presence of an insertion consisting of 24 nucleotides in the lys sequence. The coding sequences of lys and HP0339 show a high degree of homology with the coding sequence of bacteriophage T4 lysozyme. Because of this similarity, it was possible to model the three-dimensional structures of both the lys and HP0339 products.

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