1
|
Lynn BK, De Leenheer P, Schuster M. Putting theory to the test: An integrated computational/experimental chemostat model of the tragedy of the commons. PLoS One 2024; 19:e0300887. [PMID: 38598418 PMCID: PMC11006152 DOI: 10.1371/journal.pone.0300887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024] Open
Abstract
Cooperation via shared public goods is ubiquitous in nature, however, noncontributing social cheaters can exploit the public goods provided by cooperating individuals to gain a fitness advantage. Theory predicts that this dynamic can cause a Tragedy of the Commons, and in particular, a 'Collapsing' Tragedy defined as the extinction of the entire population if the public good is essential. However, there is little empirical evidence of the Collapsing Tragedy in evolutionary biology. Here, we experimentally demonstrate this outcome in a microbial model system, the public good-producing bacterium Pseudomonas aeruginosa grown in a continuous-culture chemostat. In a growth medium that requires extracellular protein digestion, we find that P. aeruginosa populations maintain a high density when entirely composed of cooperating, protease-producing cells but completely collapse when non-producing cheater cells are introduced. We formulate a mechanistic mathematical model that recapitulates experimental observations and suggests key parameters, such as the dilution rate and the cost of public good production, that define the stability of cooperative behavior. We combine model prediction with experimental validation to explain striking differences in the long-term cheater trajectories of replicate cocultures through mutational events that increase cheater fitness. Taken together, our integrated empirical and theoretical approach validates and parametrizes the Collapsing Tragedy in a microbial population, and provides a quantitative, mechanistic framework for generating testable predictions of social behavior.
Collapse
Affiliation(s)
- Bryan K. Lynn
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
| | - Patrick De Leenheer
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Mathematics, Oregon State University, Corvallis, Oregon, United States of America
| | - Martin Schuster
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| |
Collapse
|
2
|
Alfinito E, Beccaria M, Cesaria M. Cooperation in bioluminescence: understanding the role of autoinducers by a stochastic random resistor model. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:94. [PMID: 37812340 PMCID: PMC10562348 DOI: 10.1140/epje/s10189-023-00352-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/23/2023] [Indexed: 10/10/2023]
Abstract
Quorum sensing is a communication mechanism adopted by different bacterial strains for the regulation of gene transcription. It takes place through the exchange of molecules called autoinducers. Bioluminescence is an emergent threshold phenomenon shown by some bacteria strains. Its precise relationship to quorum sensing is a debated topic, particularly regarding the role of the different autoinducers used by bacteria. In this paper, assuming a direct relationship between bioluminescence and quorum sensing, we investigate the role of multiple autoinducers in the bioluminescence response of Vibrio harveyi, considered as a model bioluminescent strain, due to its quorum sensing circuitry involving an array of three different autoinducers. Experiments on mutants of this bacterium, obtained by suppression of one or more autoinducers, reveal their relative non-trivial relevance and cooperative interaction patterns. The proposed analysis is implemented on a regular lattice, whose nodes represent microbial entities equipped with charges, which represent the ability to up/down regulate the gene expression. Quorum sensing results from a Coulomb-type field, produced by the charges. In analogy with random resistor network models, the lattice is permeated by an effective current which accounts for the amount and distribution of the charges. We propose that the presence of different autoinducers correspond to a different up/down regulation of gene expression, i.e., to a different way to account for the charges. Then, by introducing a modulation of the charge dependence into the current flowing within the network, we show that it is able to describe the bioluminescence exhibited by V. harveyi mutants. Furthermore, modulation of the charge dependence allows the interactions between the different autoinducers to be taken into account, providing a prediction regarding the data obtainable under specific growth conditions.
Collapse
Affiliation(s)
- Eleonora Alfinito
- Dipartimento di Matematica e Fisica 'Ennio De Giorgi', Università del Salento, Via Arnesano, 73100, Lecce, Italy.
| | - Matteo Beccaria
- Dipartimento di Matematica e Fisica 'Ennio De Giorgi', Università del Salento, Via Arnesano, 73100, Lecce, Italy
- Istituto Nazionale di Fisica Nucleare - Sezione di Lecce, Via Arnesano, 73100, Lecce, Italy
- National Biodiversity Future Center, 90133, Palermo, Italy
| | - Maura Cesaria
- Dipartimento di Matematica e Fisica 'Ennio De Giorgi', Università del Salento, Via Arnesano, 73100, Lecce, Italy
| |
Collapse
|
3
|
Schuster M, Li C, Smith P, Kuttler C. Parameters, architecture and emergent properties of the Pseudomonas aeruginosa LasI/LasR quorum-sensing circuit. J R Soc Interface 2023; 20:20220825. [PMID: 36919437 PMCID: PMC10015328 DOI: 10.1098/rsif.2022.0825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/22/2023] [Indexed: 03/16/2023] Open
Abstract
Quorum sensing is a widespread process in bacteria that controls collective behaviours in response to cell density. Populations of cells coordinate gene expression through the perception of self-produced chemical signals. Although this process is well-characterized genetically and biochemically, quantitative information about network properties, including induction dynamics and steady-state behaviour, is scarce. Here we integrate experiments with mathematical modelling to quantitatively analyse the LasI/LasR quorum sensing pathway in the opportunistic pathogen Pseudomonas aeruginosa. We determine key kinetic parameters of the pathway and, using the parametrized model, show that quorum sensing behaves as a bistable hysteretic switch, with stable on and off states. We investigate the significance of feedback architecture and find that positive feedback on signal production is critical for induction dynamics and bistability, whereas positive feedback on receptor expression and negative feedback on signal production play a minor role. Taken together, our data-based modelling approach reveals fundamental and emergent properties of a bacterial quorum sensing circuit, and provides evidence that native quorum sensing can indeed function as the gene expression switch it is commonly perceived to be.
Collapse
Affiliation(s)
- Martin Schuster
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Christina Li
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Parker Smith
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Christina Kuttler
- Department of Mathematics, Technische Universität München, 85748 Garching, Germany
| |
Collapse
|
4
|
Rattray JB, Brown SP. Beyond Thresholds: Quorum‐Sensing as Quantitatively Varying Reaction Norms to Multiple Environmental Dimensions. Isr J Chem 2023. [DOI: 10.1002/ijch.202200109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Jennifer B. Rattray
- School of Biological Sciences Georgia Institute of Technology Atlanta GA 30332 USA
- Center for Microbial Dynamics and Infection Georgia Institute of Technology Atlanta GA 30332 USA
| | - Sam P. Brown
- School of Biological Sciences Georgia Institute of Technology Atlanta GA 30332 USA
- Center for Microbial Dynamics and Infection Georgia Institute of Technology Atlanta GA 30332 USA
| |
Collapse
|
5
|
Rattray JB, Thomas SA, Wang Y, Molotkova E, Gurney J, Varga JJ, Brown SP. Bacterial Quorum Sensing Allows Graded and Bimodal Cellular Responses to Variations in Population Density. mBio 2022; 13:e0074522. [PMID: 35583321 PMCID: PMC9239169 DOI: 10.1128/mbio.00745-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/11/2022] [Indexed: 12/20/2022] Open
Abstract
Quorum sensing (QS) is a mechanism of cell-cell communication that connects gene expression to environmental conditions (e.g., cell density) in many bacterial species, mediated by diffusible signal molecules. Current functional studies focus on qualitatively distinct QS ON/OFF states. In the context of density sensing, this view led to the adoption of a "quorum" analogy in which populations sense when they are above a sufficient density (i.e., "quorate") to efficiently turn on cooperative behaviors. This framework overlooks the potential for intermediate, graded responses to shifts in the environment. In this study, we tracked QS-regulated protease (lasB) expression and showed that Pseudomonas aeruginosa can deliver a graded behavioral response to fine-scale variation in population density, on both the population and single-cell scales. On the population scale, we saw a graded response to variation in population density (controlled by culture carrying capacity). On the single-cell scale, we saw significant bimodality at higher densities, with separate OFF and ON subpopulations that responded differentially to changes in density: a static OFF population of cells and increasing intensity of expression among the ON population of cells. Together, these results indicate that QS can tune gene expression to graded environmental change, with no critical cell mass or "quorum" at which behavioral responses are activated on either the individual-cell or population scale. In an infection context, our results indicate there is not a hard threshold separating a quorate "attack" mode from a subquorate "stealth" mode. IMPORTANCE Bacteria can be highly social, controlling collective behaviors via cell-cell communication mechanisms known as quorum sensing (QS). QS is now a large research field, yet a basic question remains unanswered: what is the environmental resolution of QS? The notion of a threshold, or "quorum," separating coordinated ON and OFF states is a central dogma in QS, but recent studies have shown heterogeneous responses at a single cell scale. Using Pseudomonas aeruginosa, we showed that populations generate graded responses to environmental variation through shifts in the proportion of cells responding and the intensity of responses. In an infection context, our results indicate that there is not a hard threshold separating a quorate "attack" mode and a subquorate "stealth" mode.
Collapse
Affiliation(s)
- Jennifer B. Rattray
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Stephen A. Thomas
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- Graduate Program in Quantitative Biosciences (QBioS), Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yifei Wang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- The Institute for Data Engineering and Science (IDEaS), Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Evgeniya Molotkova
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - James Gurney
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - John J. Varga
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sam P. Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| |
Collapse
|
6
|
Abstract
Quorum sensing is described as a widespread cell density-dependent signaling mechanism in bacteria. Groups of cells coordinate gene expression by secreting and responding to diffusible signal molecules. Theory, however, predicts that individual cells may short-circuit this mechanism by directly responding to the signals they produce irrespective of cell density. In this study, we characterize this self-sensing effect in the acyl-homoserine lactone quorum sensing system of Pseudomonas aeruginosa. We show that antiactivators, a set of proteins known to affect signal sensitivity, function to prevent self-sensing. Measuring quorum-sensing gene expression in individual cells at very low densities, we find that successive deletion of antiactivator genes qteE and qslA produces a bimodal response pattern, in which increasing proportions of constitutively induced cells coexist with uninduced cells. Comparing responses of signal-proficient and -deficient cells in cocultures, we find that signal-proficient cells show a much higher response in the antiactivator mutant background but not in the wild-type background. Our results experimentally demonstrate the antiactivator-dependent transition from group- to self-sensing in the quorum-sensing circuitry of P. aeruginosa. Taken together, these findings extend our understanding of the functional capacity of quorum sensing. They highlight the functional significance of antiactivators in the maintenance of group-level signaling and experimentally prove long-standing theoretical predictions.
Collapse
|
7
|
Ranjbaran M, Carciofi BAM, Datta AK. Engineering modeling frameworks for microbial food safety at various scales. Compr Rev Food Sci Food Saf 2021; 20:4213-4249. [PMID: 34486219 DOI: 10.1111/1541-4337.12818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 01/25/2021] [Indexed: 11/27/2022]
Abstract
The landscape of mathematical model-based understanding of microbial food safety is wide and deep, covering interdisciplinary fields of food science, microbiology, physics, and engineering. With rapidly growing interest in such model-based approaches that increasingly include more fundamental mechanisms of microbial processes, there is a need to build a general framework that steers this evolutionary process by synthesizing literature spread over many disciplines. The framework proposed here shows four interconnected, complementary levels of microbial food processes covering sub-cellular scale, microbial population scale, food scale, and human population scale (risk). A continuum of completely mechanistic to completely empirical models, widely-used and emerging, are integrated into the framework; well-known predictive microbiology modeling being a part of this spectrum. The framework emphasizes fundamentals-based approaches that should get enriched over time, such as the basic building blocks of microbial population scale processes (attachment, migration, growth, death/inactivation and communication) and of food processes (e.g., heat and moisture transfer). A spectrum of models are included, for example, microbial population modeling covers traditional predictive microbiology models to individual-based models and cellular automata. The models are shown in sufficient quantitative detail to make obvious their coupling, or their integration over various levels. Guidelines to combine sub-processes over various spatial and time scales into a complete interdisciplinary and multiphysics model (i.e., a system) are provided, covering microbial growth/inactivation/transport and physical processes such as fluid flow and heat transfer. As food safety becomes increasingly predictive at various scales, this synthesis should provide its roadmap. This big picture and framework should be futuristic in driving novel research and educational approaches.
Collapse
Affiliation(s)
- Mohsen Ranjbaran
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Bruno A M Carciofi
- Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianopolis, SC, Brazil
| | - Ashim K Datta
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| |
Collapse
|
8
|
Zhang L, Wang L, Yuan X, Zhong M, Chen H, Zhang D, Han X, Xie S, He L, Li Y, Chen F, Liu Y, Tan W. Decoding the Complex Free Radical Cascade by Using a DNA Framework-Based Artificial DNA Encoder. Angew Chem Int Ed Engl 2021; 60:10745-10755. [PMID: 33555644 DOI: 10.1002/anie.202014088] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/21/2020] [Indexed: 02/06/2023]
Abstract
DNA-based molecular communications (DMC) are critical for regulating biological networks to maintain stable organismic functions. However, the complicated, time-consuming information transmission process involved in genome-coded DMC and the limited, vulnerable decoding activity generally lead to communication impairment or failure, in response to external stimuli. Herein, we present a conceptually innovative DMC strategy mediated by the DNA framework-based artificial DNA encoder. With the free-radical cascade as a proof-of-concept study, the artificial DNA encoder shows active sensing and real-time actuation, in situ and broad free radical-decoding efficacy, as well as robust resistance to environmental noise. It can also block undesirable short-to-medium-range communications between free radicals and inflammatory networks, leading to a synergistic anti-obesity effect. The artificial DNA encoder-based DMC may be generalized to other communication systems for a variety of applications.
Collapse
Affiliation(s)
- Lili Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Linlin Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Xi Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Minjuan Zhong
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Hong Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Dailiang Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Xiaoyan Han
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Sitao Xie
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Lei He
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Yazhou Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Fengming Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Yanlan Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China.,The Cancer Hospital of the University of, Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.,Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, Alachua, FL, 32615, USA
| |
Collapse
|
9
|
Zhang L, Wang L, Yuan X, Zhong M, Chen H, Zhang D, Han X, Xie S, He L, Li Y, Chen F, Liu Y, Tan W. Decoding the Complex Free Radical Cascade by Using a DNA Framework‐Based Artificial DNA Encoder. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lili Zhang
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Linlin Wang
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Xi Yuan
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Minjuan Zhong
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Hong Chen
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Dailiang Zhang
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Xiaoyan Han
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Sitao Xie
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Lei He
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Yazhou Li
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Fengming Chen
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Yanlan Liu
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital) Institute of Basic Medicine and Cancer (IBMC) Chinese Academy of Sciences Hangzhou Zhejiang 310022 China
- Foundation for Applied Molecular Evolution 13709 Progress Boulevard Alachua FL 32615 USA
| |
Collapse
|
10
|
Ranjbaran M, Solhtalab M, Datta AK. Mechanistic modeling of light-induced chemotactic infiltration of bacteria into leaf stomata. PLoS Comput Biol 2020; 16:e1007841. [PMID: 32384085 PMCID: PMC7209104 DOI: 10.1371/journal.pcbi.1007841] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/02/2020] [Indexed: 12/04/2022] Open
Abstract
Light is one of the factors that can play a role in bacterial infiltration into leafy greens by keeping stomata open and providing photosynthetic products for microorganisms. We model chemotactic transport of bacteria within a leaf tissue in response to photosynthesis occurring within plant mesophyll. The model includes transport of carbon dioxide, oxygen, bicarbonate, sucrose/glucose, bacteria, and autoinducer-2 within the leaf tissue. Biological processes of carbon fixation in chloroplasts, and respiration in mitochondria of the plant cells, as well as motility, chemotaxis, nutrient consumption and communication in the bacterial community are considered. We show that presence of light is enough to boost bacterial chemotaxis through the stomatal opening and toward photosynthetic products within the leaf tissue. Bacterial chemotactic ability is a major player in infiltration, and plant stomatal defense in closing the stomata as a perception of microbe-associated molecular patterns is an effective way to inhibit the infiltration. Exposure to light can trigger photosynthesis in plant leaves, such as leafy-greens, and increase concentrations of photosynthetic products, such as glucose, within the leaf tissue. Bacteria existing at the leaf surfaces may respond to the available photosynthetic products and migrate into the leaf tissue by chemotaxis toward nutrient concentration gradients. Once the bacteria are inside the leaf tissue, they cannot be washed away, presenting a risk to the consumer. Here, a physics-based model for this light-driven infiltration is presented. This mechanistic model couples transport of bacteria and nutrients, and photosynthesis within a leaf tissue around one stomatal opening. The model shows that the ability of bacteria to transport via chemotaxis is a major factor in infiltration. A moderate intensity light is sufficient to promote chemotactic infiltration of bacteria on a leaf surface into its interior. Infiltration is enhanced in the presence of blue, white and red lights, and for a larger stomatal aperture.
Collapse
Affiliation(s)
- Mohsen Ranjbaran
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, United States of America
| | - Mina Solhtalab
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, United States of America
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois, United States of America
| | - Ashim K. Datta
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| |
Collapse
|
11
|
Wu S, Liu J, Liu C, Yang A, Qiao J. Quorum sensing for population-level control of bacteria and potential therapeutic applications. Cell Mol Life Sci 2020; 77:1319-1343. [PMID: 31612240 PMCID: PMC11104945 DOI: 10.1007/s00018-019-03326-8] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/13/2019] [Accepted: 09/30/2019] [Indexed: 02/07/2023]
Abstract
Quorum sensing (QS), a microbial cell-to-cell communication process, dynamically regulates a variety of metabolism and physiological activities. In this review, we provide an update on QS applications based on autoinducer molecules including acyl-homoserine lactones (AHLs), auto-inducing peptides (AIPs), autoinducer 2 (AI-2) and indole in population-level control of bacteria, and highlight the potential in developing novel clinical therapies. We summarize the development in the combination of various genetic circuits such as genetic oscillators, toggle switches and logic gates with AHL-based QS devices in Gram-negative bacteria. An overview is then offered to the state-of-the-art of much less researched applications of AIP-based QS devices with Gram-positive bacteria, followed by a review of the applications of AI-2 and indole based QS for interspecies communication among microbial communities. Building on these general-purpose QS applications, we highlight the disruptions and manipulations of QS devices as potential clinical therapies for diseases caused by biofilm formation, antibiotic resistance and the phage invasion. The last part of reviewed literature is dedicated to mathematical modelling for QS applications. Finally, the key challenges and future perspectives of QS applications in monoclonal synthetic biology and synthetic ecology are discussed.
Collapse
Affiliation(s)
- Shengbo Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
| | - Jiaheng Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China
| | - Chunjiang Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
| | - Aidong Yang
- Department of Engineering Science, University of Oxford, Oxford, OX1 3PJ, UK.
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China.
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China.
| |
Collapse
|
12
|
Li X, Zhang G, Zhu Y, Bi J, Hao H, Hou H. Effect of the luxI/R gene on AHL-signaling molecules and QS regulatory mechanism in Hafnia alvei H4. AMB Express 2019; 9:197. [PMID: 31807954 PMCID: PMC6895348 DOI: 10.1186/s13568-019-0917-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 11/22/2019] [Indexed: 01/03/2023] Open
Abstract
Hafnia alvei H4 is a bacterium subject to regulation by a N-acyl-l-homoserine lactone (AHL)-mediated quorum sensing system and is closely related to the corruption of instant sea cucumber. Studying the effect of Hafnia alvei H4 quorum sensing regulatory genes on AHLs is necessary for the quality and preservation of instant sea cucumber. In this study, the draft genome of H. alvei H4, which comprises a single chromosome of 4,687,151 bp, was sequenced and analyzed and the types of AHLs were analyzed employing thin-layer chromatography (TLC) and high resolution triple quadrupole liquid chromatography/mass spectrometry (LC/MS). Then the wild-type strain of H. alvei H4 and the luxI/R double mutant (ΔluxIR) were compared by transcriptome sequencing (RNA-seq). The results indicate that the incomplete genome sequence revealed the presence of one quorum-sensing (QS) gene set, designated as lasI/expR. Three major AHLs, N-hexanoyl-l-homoserine lactone (C6-HSL), N-butyryl-l-homoserine lactone (C4-HSL), and N-(3-oxo-octanoyl)-l-homoserine lactone (3-oxo-C8-HSL) were found, with C6-HSL being the most abundant. C6-HSL was not detected in the culture of the luxI mutant (ΔluxI) and higher levels of C4-HSL was found in the culture of the luxR mutant (ΔluxR), which suggested that the luxR gene may have a positive effect on C4-HSL production. It was also found that AHL and QS genes are closely related in the absence of luxIR double deletion. The results of this study can further elucidate at the genetic level that luxI and luxR genes are involved in the regulation of AHL.
Collapse
|
13
|
Kindler O, Pulkkinen O, Cherstvy AG, Metzler R. Burst statistics in an early biofilm quorum sensing model: the role of spatial colony-growth heterogeneity. Sci Rep 2019; 9:12077. [PMID: 31427659 PMCID: PMC6700081 DOI: 10.1038/s41598-019-48525-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 08/07/2019] [Indexed: 01/01/2023] Open
Abstract
Quorum-sensing bacteria in a growing colony of cells send out signalling molecules (so-called “autoinducers”) and themselves sense the autoinducer concentration in their vicinity. Once—due to increased local cell density inside a “cluster” of the growing colony—the concentration of autoinducers exceeds a threshold value, cells in this clusters get “induced” into a communal, multi-cell biofilm-forming mode in a cluster-wide burst event. We analyse quantitatively the influence of spatial disorder, the local heterogeneity of the spatial distribution of cells in the colony, and additional physical parameters such as the autoinducer signal range on the induction dynamics of the cell colony. Spatial inhomogeneity with higher local cell concentrations in clusters leads to earlier but more localised induction events, while homogeneous distributions lead to comparatively delayed but more concerted induction of the cell colony, and, thus, a behaviour close to the mean-field dynamics. We quantify the induction dynamics with quantifiers such as the time series of induction events and burst sizes, the grouping into induction families, and the mean autoinducer concentration levels. Consequences for different scenarios of biofilm growth are discussed, providing possible cues for biofilm control in both health care and biotechnology.
Collapse
Affiliation(s)
- Oliver Kindler
- Institute for Physics & Astronomy, University of Potsdam, D-14476, Potsdam-Golm, Germany
| | - Otto Pulkkinen
- Institute for Molecular Medicine Finland and Helsinki Institute for Information Technology, University of Helsinki, FI-00014, Helsinki, Finland
| | - Andrey G Cherstvy
- Institute for Physics & Astronomy, University of Potsdam, D-14476, Potsdam-Golm, Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam, D-14476, Potsdam-Golm, Germany.
| |
Collapse
|
14
|
Gilbert D, Heiner M, Ghanbar L, Chodak J. Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking. BMC Bioinformatics 2019; 20:173. [PMID: 30999841 PMCID: PMC6471779 DOI: 10.1186/s12859-019-2690-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Quorum sensing drives biofilm formation in bacteria in order to ensure that biofilm formation only occurs when colonies are of a sufficient size and density. This spatial behaviour is achieved by the broadcast communication of an autoinducer in a diffusion scenario. This is of interest, for example, when considering the role of gut microbiota in gut health. This behaviour occurs within the context of the four phases of bacterial growth, specifically in the exponential stage (phase 2) for autoinducer production and the stationary stage (phase 3) for biofilm formation. RESULTS We have used coloured hybrid Petri nets to step-wise develop a flexible computational model for E.coli biofilm formation driven by Autoinducer 2 (AI-2) which is easy to configure for different notions of space. The model describes the essential components of gene transcription, signal transduction, extra and intra cellular transport, as well as the two-phase nature of the system. We build on a previously published non-spatial stochastic Petri net model of AI-2 production, keeping the assumptions of a limited nutritional environment, and our spatial hybrid Petri net model of biofilm formation, first presented at the NETTAB 2017 workshop. First we consider the two models separately without space, and then combined, and finally we add space. We describe in detail our step-wise model development and validation. Our simulation results support the expected behaviour that biofilm formation is increased in areas of higher bacterial colony size and density. Our analysis techniques include behaviour checking based on linear time temporal logic. CONCLUSIONS The advantages of our modelling and analysis approach are the description of quorum sensing and associated biofilm formation over two phases of bacterial growth, taking into account bacterial spatial distribution using a flexible and easy to maintain computational model. All computational results are reproducible.
Collapse
Affiliation(s)
- David Gilbert
- Department of Computer Science, Brunel University London, Uxbridge, UB8 3PH UK
| | - Monika Heiner
- Department of Computer Science, Brunel University London, Uxbridge, UB8 3PH UK
- Computer Science Department, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, D-03046 Germany
| | - Leila Ghanbar
- Department of Computer Science, Brunel University London, Uxbridge, UB8 3PH UK
| | - Jacek Chodak
- Computer Science Department, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, D-03046 Germany
| |
Collapse
|
15
|
Cell-cell communication enhances bacterial chemotaxis toward external attractants. Sci Rep 2017; 7:12855. [PMID: 28993669 PMCID: PMC5634484 DOI: 10.1038/s41598-017-13183-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/19/2017] [Indexed: 11/22/2022] Open
Abstract
Bacteria are able to coordinate their movement, growth and biochemical activities through cell-cell communication. While the biophysical mechanism of bacterial chemotaxis has been well understood in individual cells, the role of communication in the chemotaxis of bacterial populations is not clear. Here we report experimental evidence for cell-cell communication that significantly enhances the chemotactic migration of bacterial populations, a finding that we further substantiate using numerical simulations. Using a microfluidic approach, we find that E. coli cells respond to the gradient of chemoattractant not only by biasing their own random-walk swimming pattern through the well-understood intracellular chemotaxis signaling, but also by actively secreting a chemical signal into the extracellular medium, possibly through a hitherto unknown communication signal transduction pathway. This extracellular signaling molecule is a strong chemoattractant that attracts distant cells to the food source. The observed behavior may represent a common evolved solution to accelerate the function of biochemical networks of interacting cells.
Collapse
|
16
|
Zúñiga A, Donoso RA, Ruiz D, Ruz GA, González B. Quorum-Sensing Systems in the Plant Growth-Promoting Bacterium Paraburkholderia phytofirmans PsJN Exhibit Cross-Regulation and Are Involved in Biofilm Formation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:557-565. [PMID: 28548604 DOI: 10.1094/mpmi-01-17-0008-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Quorum-sensing systems play important roles in host colonization and host establishment of Burkholderiales species. Beneficial Paraburkholderia species share a conserved quorum-sensing (QS) system, designated BraI/R, that controls different phenotypes. In this context, the plant growth-promoting bacterium Paraburkholderia phytofirmans PsJN possesses two different homoserine lactone QS systems BpI.1/R.1 and BpI.2/R.2 (BraI/R-like QS system). The BpI.1/R.1 QS system was previously reported to be important to colonize and produce beneficial effects in Arabidopsis thaliana plants. Here, we analyzed the temporal variations of the QS gene transcript levels in the wild-type strain colonizing plant roots. The gene expression patterns showed relevant differences in both QS systems compared with the wild-type strain in the unplanted control treatment. The gene expression data were used to reconstruct a regulatory network model of QS systems in P. phytofirmans PsJN, using a Boolean network model. Also, we examined the phenotypic traits and transcript levels of genes involved in QS systems, using P. phytofirmans mutants in homoserine lactone synthases genes. We observed that the BpI.1/R.1 QS system regulates biofilm formation production in strain PsJN and this phenotype was associated with the lower expression of a specific extracytoplasmic function sigma factor ecf26.1 gene (implicated in biofilm formation) in the bpI.1 mutant strain.
Collapse
Affiliation(s)
- Ana Zúñiga
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Millennium Nucleus Center for Plant Systems and Synthetic Biology, and Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Raúl A Donoso
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Millennium Nucleus Center for Plant Systems and Synthetic Biology, and Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Daniela Ruiz
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Millennium Nucleus Center for Plant Systems and Synthetic Biology, and Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Gonzalo A Ruz
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Millennium Nucleus Center for Plant Systems and Synthetic Biology, and Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Bernardo González
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Millennium Nucleus Center for Plant Systems and Synthetic Biology, and Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| |
Collapse
|
17
|
Mathematical Modelling of Bacterial Quorum Sensing: A Review. Bull Math Biol 2016; 78:1585-639. [PMID: 27561265 DOI: 10.1007/s11538-016-0160-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 03/15/2016] [Indexed: 12/21/2022]
Abstract
Bacterial quorum sensing (QS) refers to the process of cell-to-cell bacterial communication enabled through the production and sensing of the local concentration of small molecules called autoinducers to regulate the production of gene products (e.g. enzymes or virulence factors). Through autoinducers, bacteria interact with individuals of the same species, other bacterial species, and with their host. Among QS-regulated processes mediated through autoinducers are aggregation, biofilm formation, bioluminescence, and sporulation. Autoinducers are therefore "master" regulators of bacterial lifestyles. For over 10 years, mathematical modelling of QS has sought, in parallel to experimental discoveries, to elucidate the mechanisms regulating this process. In this review, we present the progress in mathematical modelling of QS, highlighting the various theoretical approaches that have been used and discussing some of the insights that have emerged. Modelling of QS has benefited almost from the onset of the involvement of experimentalists, with many of the papers which we review, published in non-mathematical journals. This review therefore attempts to give a broad overview of the topic to the mathematical biology community, as well as the current modelling efforts and future challenges.
Collapse
|
18
|
Ramsay JP, Ronson CW. Silencing quorum sensing and ICE mobility through antiactivation and ribosomal frameshifting. Mob Genet Elements 2015; 5:103-108. [PMID: 26942047 PMCID: PMC4755241 DOI: 10.1080/2159256x.2015.1107177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 10/06/2015] [Accepted: 10/06/2015] [Indexed: 01/27/2023] Open
Abstract
Mobile genetic elements run an evolutionary gauntlet to maintain their mobility in the face of selection against their selfish dissemination but, paradoxically, they can accelerate the adaptability of bacteria through the gene-transfer events that they facilitate. These temporally conflicting evolutionary forces have shaped exquisite regulation systems that silence mobility and maximize the competitive fitness of the host bacterium, but maintain the ability of the element to deliver itself to a new host should the opportunity arise. Here we review the excision regulation system of the Mesorhizobium loti symbiosis island ICEMlSymR7A, a 502-kb integrative and conjugative element (ICE) capable of converting non-symbiotic mesorhizobia into plant symbionts. ICEMlSymR7A excision is activated by quorum sensing, however, both quorum sensing and excision are strongly repressed in the vast majority of cells by dual-target antiactivation and programmed ribosomal-frameshifting mechanisms. We examine these recently discovered regulatory features under the light of natural selection and discuss common themes that can be drawn from recent developments in ICE biology.
Collapse
Affiliation(s)
- Joshua P Ramsay
- School of Biomedical Sciences; Curtin University ; Perth, Australia
| | - Clive W Ronson
- Department of Microbiology and Immunology; University of Otago ; Dunedin, New Zealand
| |
Collapse
|
19
|
Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing-activated transfer of a mobile genetic element. Proc Natl Acad Sci U S A 2015; 112:4104-9. [PMID: 25787256 DOI: 10.1073/pnas.1501574112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Symbiosis islands are integrative and conjugative mobile genetic elements that convert nonsymbiotic rhizobia into nitrogen-fixing symbionts of leguminous plants. Excision of the Mesorhizobium loti symbiosis island ICEMlSym(R7A) is indirectly activated by quorum sensing through TraR-dependent activation of the excisionase gene rdfS. Here we show that a +1 programmed ribosomal frameshift (PRF) fuses the coding sequences of two TraR-activated genes, msi172 and msi171, producing an activator of rdfS expression named Frameshifted excision activator (FseA). Mass-spectrometry and mutational analyses indicated that the PRF occurred through +1 slippage of the tRNA(phe) from UUU to UUC within a conserved msi172-encoded motif. FseA activated rdfS expression in the absence of ICEMlSym(R7A), suggesting that it directly activated rdfS transcription, despite being unrelated to any characterized DNA-binding proteins. Bacterial two-hybrid and gene-reporter assays demonstrated that FseA was also bound and inhibited by the ICEMlSym(R7A)-encoded quorum-sensing antiactivator QseM. Thus, activation of ICEMlSym(R7A) excision is counteracted by TraR antiactivation, ribosomal frameshifting, and FseA antiactivation. This robust suppression likely dampens the inherent biological noise present in the quorum-sensing autoinduction circuit and ensures that ICEMlSym(R7A) transfer only occurs in a subpopulation of cells in which both qseM expression is repressed and FseA is translated. The architecture of the ICEMlSym(R7A) transfer regulatory system provides an example of how a set of modular components have assembled through evolution to form a robust genetic toggle that regulates gene transcription and translation at both single-cell and cell-population levels.
Collapse
|
20
|
Popat R, Cornforth DM, McNally L, Brown SP. Collective sensing and collective responses in quorum-sensing bacteria. J R Soc Interface 2015; 12:20140882. [PMID: 25505130 PMCID: PMC4305403 DOI: 10.1098/rsif.2014.0882] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/12/2014] [Indexed: 11/21/2022] Open
Abstract
Bacteria often face fluctuating environments, and in response many species have evolved complex decision-making mechanisms to match their behaviour to the prevailing conditions. Some environmental cues provide direct and reliable information (such as nutrient concentrations) and can be responded to individually. Other environmental parameters are harder to infer and require a collective mechanism of sensing. In addition, some environmental challenges are best faced by a group of cells rather than an individual. In this review, we discuss how bacteria sense and overcome environmental challenges as a group using collective mechanisms of sensing, known as 'quorum sensing' (QS). QS is characterized by the release and detection of small molecules, potentially allowing individuals to infer environmental parameters such as density and mass transfer. While a great deal of the molecular mechanisms of QS have been described, there is still controversy over its functional role. We discuss what QS senses and how, what it controls and why, and how social dilemmas shape its evolution. Finally, there is a growing focus on the use of QS inhibitors as antibacterial chemotherapy. We discuss the claim that such a strategy could overcome the evolution of resistance. By linking existing theoretical approaches to data, we hope this review will spur greater collaboration between experimental and theoretical researchers.
Collapse
Affiliation(s)
- R Popat
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - D M Cornforth
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK Molecular Biosciences, University of Texas at Austin, 2500 Speedway NMS 3.254, Austin, TX 78712, USA
| | - L McNally
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - S P Brown
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| |
Collapse
|
21
|
Lui LT, Xue X, Sui C, Brown A, Pritchard DI, Halliday N, Winzer K, Howdle SM, Fernandez-Trillo F, Krasnogor N, Alexander C. Bacteria clustering by polymers induces the expression of quorum-sensing-controlled phenotypes. Nat Chem 2013; 5:1058-65. [PMID: 24256871 DOI: 10.1038/nchem.1793] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 10/04/2013] [Indexed: 12/28/2022]
Abstract
Bacteria deploy a range of chemistries to regulate their behaviour and respond to their environment. Quorum sensing is one method by which bacteria use chemical reactions to modulate pre-infection behaviour such as surface attachment. Polymers that can interfere with bacterial adhesion or the chemical reactions used for quorum sensing are therefore a potential means to control bacterial population responses. Here, we report how polymeric 'bacteria sequestrants', designed to bind to bacteria through electrostatic interactions and therefore inhibit bacterial adhesion to surfaces, induce the expression of quorum-sensing-controlled phenotypes as a consequence of cell clustering. A combination of polymer and analytical chemistry, biological assays and computational modelling has been used to characterize the feedback between bacteria clustering and quorum sensing signalling. We have also derived design principles and chemical strategies for controlling bacterial behaviour at the population level.
Collapse
Affiliation(s)
- Leong T Lui
- School of Computer Science, The University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Brown D. Linking Molecular and Population Processes in Mathematical Models of Quorum Sensing. Bull Math Biol 2013; 75:1813-39. [DOI: 10.1007/s11538-013-9870-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 06/20/2013] [Indexed: 12/21/2022]
|
23
|
The organization of the quorum sensing luxI/R family genes in Burkholderia. Int J Mol Sci 2013; 14:13727-47. [PMID: 23820583 PMCID: PMC3742214 DOI: 10.3390/ijms140713727] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 06/20/2013] [Accepted: 06/24/2013] [Indexed: 12/12/2022] Open
Abstract
Members of the Burkholderia genus of Proteobacteria are capable of living freely in the environment and can also colonize human, animal and plant hosts. Certain members are considered to be clinically important from both medical and veterinary perspectives and furthermore may be important modulators of the rhizosphere. Quorum sensing via N-acyl homoserine lactone signals (AHL QS) is present in almost all Burkholderia species and is thought to play important roles in lifestyle changes such as colonization and niche invasion. Here we present a census of AHL QS genes retrieved from public databases and indicate that the local arrangement (topology) of QS genes, their location within chromosomes and their gene neighborhoods show characteristic patterns that differ between the known Burkholderia clades. In sequence phylogenies, AHL QS genes seem to cluster according to the local gene topology rather than according to the species, which suggests that the basic topology types were present prior to the appearance of current Burkholderia species. The data are available at http://net.icgeb.org/burkholderia/.
Collapse
|
24
|
Fujimoto K, Sawai S. A design principle of group-level decision making in cell populations. PLoS Comput Biol 2013; 9:e1003110. [PMID: 23825937 PMCID: PMC3694814 DOI: 10.1371/journal.pcbi.1003110] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 05/05/2013] [Indexed: 11/19/2022] Open
Abstract
Populations of cells often switch states as a group to cope with environmental changes such as nutrient availability and cell density. Although the gene circuits that underlie the switches are well understood at the level of single cells, the ways in which such circuits work in concert among many cells to support group-level switches are not fully explored. Experimental studies of microbial quorum sensing show that group-level changes in cellular states occur in either a graded or an all-or-none fashion. Here, we show through numerical simulations and mathematical analysis that these behaviors generally originate from two distinct forms of bistability. The choice of bistability is uniquely determined by a dimensionless parameter that compares the synthesis and the transport of the inducing molecules. The role of the parameter is universal, such that it not only applies to the autoinducing circuits typically found in bacteria but also to the more complex gene circuits involved in transmembrane receptor signaling. Furthermore, in gene circuits with negative feedback, the same dimensionless parameter determines the coherence of group-level transitions from quiescence to a rhythmic state. The set of biochemical parameters in bacterial quorum-sensing circuits appear to be tuned so that the cells can use either type of transition. The design principle identified here serves as the basis for the analysis and control of cellular collective decision making. Although the genetic circuits underlying state switching at the single-cell level are well understood, how such circuits work in concert among many cells to support the population-level switching of cellular behaviors is not fully explored. Experiments using microbial signaling systems show that group-level changes in cellular state occur in either a graded or an all-or-none fashion. We show that the type of group-level decision making used by populations is uniquely determined by a single dimensionless parameter that compares the quorum-signaling molecules accumulated within the cells with those secreted by the population. Bacterial quorum-sensing circuits appear to be tuned so that the cells can convert between the two types of decision-making in response to slight biochemical variations. Furthermore, the role of the parameter is universal such that it not only applies to the autoinducing circuits typically found in bacteria but also to the more complex gene circuits involved in transmembrane receptor signaling and negative feedback. The design principle that we describe thus serves as the basis for the analysis and control of collective cellular decision making in general.
Collapse
Affiliation(s)
- Koichi Fujimoto
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
| | | |
Collapse
|
25
|
Hellen EH, Dana SK, Zhurov B, Volkov E. Electronic implementation of a repressilator with quorum sensing feedback. PLoS One 2013; 8:e62997. [PMID: 23658793 PMCID: PMC3642084 DOI: 10.1371/journal.pone.0062997] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 04/01/2013] [Indexed: 11/18/2022] Open
Abstract
We investigate the dynamics of a synthetic genetic repressilator with quorum sensing feedback. In a basic genetic ring oscillator network in which three genes inhibit each other in unidirectional manner, an additional quorum sensing feedback loop stimulates the activity of a chosen gene providing competition between inhibitory and stimulatory activities localized in that gene. Numerical simulations show several interesting dynamics, multi-stability of limit cycle with stable steady-state, multi-stability of different stable steady-states, limit cycle with period-doubling and reverse period-doubling, and infinite period bifurcation transitions for both increasing and decreasing strength of quorum sensing feedback. We design an electronic analog of the repressilator with quorum sensing feedback and reproduce, in experiment, the numerically predicted dynamical features of the system. Noise amplification near infinite period bifurcation is also observed. An important feature of the electronic design is the accessibility and control of the important system parameters.
Collapse
Affiliation(s)
- Edward H Hellen
- Department of Physics & Astronomy, University of North Carolina Greensboro, Greensboro, North Carolina, United States of America.
| | | | | | | |
Collapse
|
26
|
Ramsay JP, Major AS, Komarovsky VM, Sullivan JT, Dy RL, Hynes MF, Salmond GPC, Ronson CW. A widely conserved molecular switch controls quorum sensing and symbiosis island transfer inMesorhizobium lotithrough expression of a novel antiactivator. Mol Microbiol 2012; 87:1-13. [DOI: 10.1111/mmi.12079] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua P. Ramsay
- Department of Microbiology and Immunology; University of Otago; PO Box 56; Dunedin; New Zealand
| | - Anthony S. Major
- Department of Microbiology and Immunology; University of Otago; PO Box 56; Dunedin; New Zealand
| | - Victor M. Komarovsky
- Department of Microbiology and Immunology; University of Otago; PO Box 56; Dunedin; New Zealand
| | - John T. Sullivan
- Department of Microbiology and Immunology; University of Otago; PO Box 56; Dunedin; New Zealand
| | - Ron L. Dy
- Department of Microbiology and Immunology; University of Otago; PO Box 56; Dunedin; New Zealand
| | - Michael F. Hynes
- Department of Biological Sciences; University of Calgary; Calgary; Canada; T2N 1N4
| | | | - Clive W. Ronson
- Department of Microbiology and Immunology; University of Otago; PO Box 56; Dunedin; New Zealand
| |
Collapse
|
27
|
Classifying the topology of AHL-driven quorum sensing circuits in proteobacterial genomes. SENSORS 2012; 12:5432-44. [PMID: 22778593 PMCID: PMC3386692 DOI: 10.3390/s120505432] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 03/24/2012] [Accepted: 04/26/2012] [Indexed: 12/04/2022]
Abstract
Virulence and adaptability of many Gram-negative bacterial species are associated with an N-acylhomoserine lactone (AHL) gene regulation mechanism called quorum sensing (QS). The arrangement of quorum sensing genes is variable throughout bacterial genomes, although there are unifying themes that are common among the various topological arrangements. A bioinformatics survey of 1,403 complete bacterial genomes revealed characteristic gene topologies in 152 genomes that could be classified into 16 topological groups. We developed a concise notation for the patterns and show that the sequences of LuxR regulators and LuxI autoinducer synthase proteins cluster according to the topological patterns. The annotated topologies are deposited online with links to sequences and genome annotations at http://bacteria.itk.ppke.hu/QStopologies/.
Collapse
|
28
|
Hense BA, Müller J, Kuttler C, Hartmann A. Spatial heterogeneity of autoinducer regulation systems. SENSORS 2012; 12:4156-71. [PMID: 22666024 PMCID: PMC3355405 DOI: 10.3390/s120404156] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 03/15/2012] [Accepted: 03/21/2012] [Indexed: 12/25/2022]
Abstract
Autoinducer signals enable coordinated behaviour of bacterial populations, a phenomenon originally described as quorum sensing. Autoinducer systems are often controlled by environmental substances as nutrients or secondary metabolites (signals) from neighbouring organisms. In cell aggregates and biofilms gradients of signals and environmental substances emerge. Mathematical modelling is used to analyse the functioning of the system. We find that the autoinducer regulation network generates spatially heterogeneous behaviour, up to a kind of multicellularity-like division of work, especially under nutrient-controlled conditions. A hybrid push/pull concept is proposed to explain the ecological function. The analysis allows to explain hitherto seemingly contradicting experimental findings.
Collapse
Affiliation(s)
- Burkhard A. Hense
- Institute of Biomathematics and Biometry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +49-89-3187-4035; Fax: +49-89-3187-3029
| | - Johannes Müller
- Department of Mathematics, Technische Universität München, Boltzmannstraße 3, 85748 Garching, Germany; E-Mails: (J.M.); (C.K.)
| | - Christina Kuttler
- Department of Mathematics, Technische Universität München, Boltzmannstraße 3, 85748 Garching, Germany; E-Mails: (J.M.); (C.K.)
| | - Anton Hartmann
- Research Unit Microbe-Plant Interactions, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; E-Mail:
| |
Collapse
|
29
|
Gelencsér Z, Galbáts B, Gonzalez JF, Choudhary KS, Hudaiberdiev S, Venturi V, Pongor S. Chromosomal Arrangement of AHL-Driven Quorum Sensing Circuits in Pseudomonas. ISRN MICROBIOLOGY 2012; 2012:484176. [PMID: 23724324 PMCID: PMC3658600 DOI: 10.5402/2012/484176] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 11/16/2011] [Indexed: 12/31/2022]
Abstract
Pseudomonas spp. are able to colonize a large variety of environments due to their wide adaptability which is also associated with an N-acyl homoserine lactone (AHL) gene regulation mechanism called quorum sensing (QS). In this article we present a systematic overview of the genomic arrangement patterns of quorum sensing genes found in Pseudomonas and compare the topologies with those found in other bacterial genomes. We find that the topological arrangement of QS genes is more variable than previously thought but there are a few unifying features that occur in many of the topological arrangements. We hypothesize that the negative regulators of QS that are often found between the canonical luxR/ and luxI-family genes may be crucial for stabilizing the output of QS circuits.
Collapse
Affiliation(s)
- Zsolt Gelencsér
- Faculty of Information Technology, Pázmány Péter Catholic University, Práter u. 50/a, 1083 Budapest, Hungary
| | | | | | | | | | | | | |
Collapse
|