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Spatially-resolved metabolic cooperativity within dense bacterial colonies.

Cole JA, Kohler L, Hedhli J, Luthey-Schulten Z - BMC Syst Biol (2015)

Bottom Line: Our results are supported by imaging experiments involving strains of fluorescently-labeled E. coli.The spatial patterns of fluorescence within these experimental colonies identify cells with upregulated genes associated with acetate crossfeeding and are in excellent agreement with the predictions.The acetate crossfeeding we see has a direct analogue in a form of lactate crossfeeding observed in certain forms of cancer, and we anticipate future application of our methodology to models of tissues and tumors.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, University of Illinois, 1110 W. Green St., Urbana, 61801, IL, USA. zan@illinois.edu.

ABSTRACT

Background: The exchange of metabolites and the reprogramming of metabolism in response to shifting microenvironmental conditions can drive subpopulations of cells within colonies toward divergent behaviors. Understanding the interactions of these subpopulations-their potential for competition as well as cooperation-requires both a metabolic model capable of accounting for a wide range of environmental conditions, and a detailed dynamic description of the cells' shared extracellular space.

Results: Here we show that a cell's position within an in silico Escherichia coli colony grown on glucose minimal agar can drastically affect its metabolism: "pioneer" cells at the outer edge engage in rapid growth that expands the colony, while dormant cells in the interior separate two spatially distinct subpopulations linked by a cooperative form of acetate crossfeeding that has so far gone unnoticed. Our hybrid simulation technique integrates 3D reaction-diffusion modeling with genome-scale flux balance analysis (FBA) to describe the position-dependent metabolism and growth of cells within a colony. Our results are supported by imaging experiments involving strains of fluorescently-labeled E. coli. The spatial patterns of fluorescence within these experimental colonies identify cells with upregulated genes associated with acetate crossfeeding and are in excellent agreement with the predictions. Furthermore, the height-to-width ratios of both the experimental and simulated colonies are in good agreement over a growth period of 48 hours.

Conclusions: Our modeling paradigm can accurately reproduce a number of known features of E. coli colony growth, as well as predict a novel one that had until now gone unrecognized. The acetate crossfeeding we see has a direct analogue in a form of lactate crossfeeding observed in certain forms of cancer, and we anticipate future application of our methodology to models of tissues and tumors.

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Metabolic behaviors within the “unregulated” and “regulated” colony models.(A) The unregulated model in cross-section after 32 hours of growth; cells were assumed to engage in their own optimal metabolism solely in response to the metabolites available. (B) The regulated model in cross-section after 32 hours of growth; cells were allowed to be in either a glucose-consuming or acetate-consuming state. (C) Cartoon of E. coli central metabolism. The purple color indicates flux through the metabolic network. Some cells of the unregulated model were predicted to engage in simultaneous glucose and acetate consumption; this highlights the necessity of accounting for resource regulation within the simulations. (D) Acetate production within both models occurred near the agar in the anoxic interior of the colony; there glucose was available but the lack of oxygen prevented use of the TCA cycle and electron transport chain. (E) Acetate consumption occurred as a thin dome within the unregulated model and as a wider and more diffuse dome in the regulated model. Also indicated are the Acetyl-CoA Synthase, Malate Synthase, and Isocitrate Lyase reaction steps. These are associated with acetate consumption and are catalyzed by Acs, AceB, and AceA (which is cotranscribed with with AceB in the aceBAK operon), respectively. (F) Oxidative phosphorylation occurred near the agar at the outer edge of the colony.
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Fig2: Metabolic behaviors within the “unregulated” and “regulated” colony models.(A) The unregulated model in cross-section after 32 hours of growth; cells were assumed to engage in their own optimal metabolism solely in response to the metabolites available. (B) The regulated model in cross-section after 32 hours of growth; cells were allowed to be in either a glucose-consuming or acetate-consuming state. (C) Cartoon of E. coli central metabolism. The purple color indicates flux through the metabolic network. Some cells of the unregulated model were predicted to engage in simultaneous glucose and acetate consumption; this highlights the necessity of accounting for resource regulation within the simulations. (D) Acetate production within both models occurred near the agar in the anoxic interior of the colony; there glucose was available but the lack of oxygen prevented use of the TCA cycle and electron transport chain. (E) Acetate consumption occurred as a thin dome within the unregulated model and as a wider and more diffuse dome in the regulated model. Also indicated are the Acetyl-CoA Synthase, Malate Synthase, and Isocitrate Lyase reaction steps. These are associated with acetate consumption and are catalyzed by Acs, AceB, and AceA (which is cotranscribed with with AceB in the aceBAK operon), respectively. (F) Oxidative phosphorylation occurred near the agar at the outer edge of the colony.

Mentions: Initially, simulations were performed without any form of regulation. The cells were assumed to engage in the metabolism that optimized growth solely in response to the substrates available (see Figure 2A). A form of cooperative crossfeeding was found to emerge within the simulated colony wherein one subpopulation produced acetate while another consumed it. This behavior resulted predominantly from oxygen depletion in the colony interior. The penetration depth of oxygen (as measured near the agar surface) was calculated to be between 40 and 50 μm—in strong agreement with previous experimental and theoretical values [13,28]. Beyond this depth, extreme hypoxia prohibited cells from making use of the tricarboxylic acid cycle (TCA) and electron transport chain, and as a result they engaged in a form of fermentative metabolism that produced acetate as a byproduct (see Figure 2A, green region). Because the availability of glucose fell dramatically with height above the agar, these cells formed a broad flat disk near the base of the colony. As the acetate diffused outward, some of it was taken up by aerobic cells nearer the periphery, which formed a thin shell of syntrophic acetate-consumers (see Figure 2A, red region). This shell was approximately 20 μm thick and accounted for a colony-wide average acetate uptake rate of about 1.32 mmol gDwt −1 hr −1 at 36 hours of simulation time. This was nearly 85% of the colony’s average acetate production rate. Because crossfeeding among E. coli is generally associated with either multi-species consortium or long-term evolutionary experiments where genetically distinct crossfeeding sub-strains arise over many generations [29], its emergence within an isogenic colony on time scales as short as a few days is of particular interest.Figure 2


Spatially-resolved metabolic cooperativity within dense bacterial colonies.

Cole JA, Kohler L, Hedhli J, Luthey-Schulten Z - BMC Syst Biol (2015)

Metabolic behaviors within the “unregulated” and “regulated” colony models.(A) The unregulated model in cross-section after 32 hours of growth; cells were assumed to engage in their own optimal metabolism solely in response to the metabolites available. (B) The regulated model in cross-section after 32 hours of growth; cells were allowed to be in either a glucose-consuming or acetate-consuming state. (C) Cartoon of E. coli central metabolism. The purple color indicates flux through the metabolic network. Some cells of the unregulated model were predicted to engage in simultaneous glucose and acetate consumption; this highlights the necessity of accounting for resource regulation within the simulations. (D) Acetate production within both models occurred near the agar in the anoxic interior of the colony; there glucose was available but the lack of oxygen prevented use of the TCA cycle and electron transport chain. (E) Acetate consumption occurred as a thin dome within the unregulated model and as a wider and more diffuse dome in the regulated model. Also indicated are the Acetyl-CoA Synthase, Malate Synthase, and Isocitrate Lyase reaction steps. These are associated with acetate consumption and are catalyzed by Acs, AceB, and AceA (which is cotranscribed with with AceB in the aceBAK operon), respectively. (F) Oxidative phosphorylation occurred near the agar at the outer edge of the colony.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4376365&req=5

Fig2: Metabolic behaviors within the “unregulated” and “regulated” colony models.(A) The unregulated model in cross-section after 32 hours of growth; cells were assumed to engage in their own optimal metabolism solely in response to the metabolites available. (B) The regulated model in cross-section after 32 hours of growth; cells were allowed to be in either a glucose-consuming or acetate-consuming state. (C) Cartoon of E. coli central metabolism. The purple color indicates flux through the metabolic network. Some cells of the unregulated model were predicted to engage in simultaneous glucose and acetate consumption; this highlights the necessity of accounting for resource regulation within the simulations. (D) Acetate production within both models occurred near the agar in the anoxic interior of the colony; there glucose was available but the lack of oxygen prevented use of the TCA cycle and electron transport chain. (E) Acetate consumption occurred as a thin dome within the unregulated model and as a wider and more diffuse dome in the regulated model. Also indicated are the Acetyl-CoA Synthase, Malate Synthase, and Isocitrate Lyase reaction steps. These are associated with acetate consumption and are catalyzed by Acs, AceB, and AceA (which is cotranscribed with with AceB in the aceBAK operon), respectively. (F) Oxidative phosphorylation occurred near the agar at the outer edge of the colony.
Mentions: Initially, simulations were performed without any form of regulation. The cells were assumed to engage in the metabolism that optimized growth solely in response to the substrates available (see Figure 2A). A form of cooperative crossfeeding was found to emerge within the simulated colony wherein one subpopulation produced acetate while another consumed it. This behavior resulted predominantly from oxygen depletion in the colony interior. The penetration depth of oxygen (as measured near the agar surface) was calculated to be between 40 and 50 μm—in strong agreement with previous experimental and theoretical values [13,28]. Beyond this depth, extreme hypoxia prohibited cells from making use of the tricarboxylic acid cycle (TCA) and electron transport chain, and as a result they engaged in a form of fermentative metabolism that produced acetate as a byproduct (see Figure 2A, green region). Because the availability of glucose fell dramatically with height above the agar, these cells formed a broad flat disk near the base of the colony. As the acetate diffused outward, some of it was taken up by aerobic cells nearer the periphery, which formed a thin shell of syntrophic acetate-consumers (see Figure 2A, red region). This shell was approximately 20 μm thick and accounted for a colony-wide average acetate uptake rate of about 1.32 mmol gDwt −1 hr −1 at 36 hours of simulation time. This was nearly 85% of the colony’s average acetate production rate. Because crossfeeding among E. coli is generally associated with either multi-species consortium or long-term evolutionary experiments where genetically distinct crossfeeding sub-strains arise over many generations [29], its emergence within an isogenic colony on time scales as short as a few days is of particular interest.Figure 2

Bottom Line: Our results are supported by imaging experiments involving strains of fluorescently-labeled E. coli.The spatial patterns of fluorescence within these experimental colonies identify cells with upregulated genes associated with acetate crossfeeding and are in excellent agreement with the predictions.The acetate crossfeeding we see has a direct analogue in a form of lactate crossfeeding observed in certain forms of cancer, and we anticipate future application of our methodology to models of tissues and tumors.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, University of Illinois, 1110 W. Green St., Urbana, 61801, IL, USA. zan@illinois.edu.

ABSTRACT

Background: The exchange of metabolites and the reprogramming of metabolism in response to shifting microenvironmental conditions can drive subpopulations of cells within colonies toward divergent behaviors. Understanding the interactions of these subpopulations-their potential for competition as well as cooperation-requires both a metabolic model capable of accounting for a wide range of environmental conditions, and a detailed dynamic description of the cells' shared extracellular space.

Results: Here we show that a cell's position within an in silico Escherichia coli colony grown on glucose minimal agar can drastically affect its metabolism: "pioneer" cells at the outer edge engage in rapid growth that expands the colony, while dormant cells in the interior separate two spatially distinct subpopulations linked by a cooperative form of acetate crossfeeding that has so far gone unnoticed. Our hybrid simulation technique integrates 3D reaction-diffusion modeling with genome-scale flux balance analysis (FBA) to describe the position-dependent metabolism and growth of cells within a colony. Our results are supported by imaging experiments involving strains of fluorescently-labeled E. coli. The spatial patterns of fluorescence within these experimental colonies identify cells with upregulated genes associated with acetate crossfeeding and are in excellent agreement with the predictions. Furthermore, the height-to-width ratios of both the experimental and simulated colonies are in good agreement over a growth period of 48 hours.

Conclusions: Our modeling paradigm can accurately reproduce a number of known features of E. coli colony growth, as well as predict a novel one that had until now gone unrecognized. The acetate crossfeeding we see has a direct analogue in a form of lactate crossfeeding observed in certain forms of cancer, and we anticipate future application of our methodology to models of tissues and tumors.

Show MeSH
Related in: MedlinePlus