Availability of the Molecular Switch XylR Controls Phenotypic Heterogeneity and Lag Duration during Escherichia coli Adaptation from Glucose to Xylose

Barthe, Manon; Tchouanti, Josué; Gomes, Pedro; Bideaux, Carine; Lestrade, Delphine; Graham, C. D.; Steyer, Jean-Philippe; Harmand, Jérôme; Gorret, Nathalie; Cocaign‐Bousquet, Muriel; Enjalbert, Brice

doi:10.1128/mbio.02938-20

Cited by 9 publications

(10 citation statements)

References 64 publications

(98 reference statements)

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“…An invader either replaces the resident, coexists with it, or is unable to invade. (b) Growth rates of the 13 laboratory E. coli strains on glucose (blue) and xylose (green), obtained from Barthe et al 46 . Note that one of the strains is anomalous.…”

Section: Discussionmentioning

confidence: 99%

“…Pairwise invasions. To simulate pairwise invasions of some realistic examples, we took 13 specific E. coli strains, whose diauxic growth on glucose and xylose were experimentally measured 46 .…”

Section: Methodsmentioning

confidence: 99%

“…al. 46 ). These strains represented a much less diverse pool than the one we had assumed so far, and thus all had the same preference order, preferring glucose over xylose (Fig.…”

Section: Diauxic Lags Promote Complementarity Coexistence and Multistabilitymentioning

confidence: 99%

“…We also sampled the diauxic lags, which is the 785 time it takes for a species to switch from consuming glucose to xylose, once glucose is depleted, from a uniform distribution between 0 hr and 1 hr. Other parameters, such as the growth rates and yields, were obtained from the experimental results, where the strains grew on a medium of 12.5% glucose and 87.5% xylose 46 . 790 We used the same ratio in our simulations.…”

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confidence: 99%

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Complementary resource preferences spontaneously emerge in diauxic microbial communities

Wang

Goyal

Dubinkina

et al. 2021

Preprint

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Most microbes grow diauxically, utilizing the available resources one at a time rather than simultaneously. The properties of communities of microbes growing diauxically remain poorly understood, largely due to a lack of theory and models of such communities. Here, we develop and study a minimal model of diauxic microbial communities assembling in a serially diluted culture. We find that community assembly repeatably and spontaneously leads to communities with complementary resource preferences i.e., communities where species prefer different resources as their top choice. Simulations and theory explain that the emergence of complementarity is driven by the disproportionate contribution of the top choice resource to the growth of a species. Additionally, we develop a geometric approach for analyzing serially diluted communities, with or without diauxie, which intuitively explains several additional emergent community properties, such as the apparent lack of species which grow fastest on a resource other than their most preferred resource. Overall, our work provides testable predictions for the assembly of natural as well as synthetic communities of diauxically shifting microbes.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…al. 46 ). These strains represented a much less diverse pool than the one we had assumed so far, and thus all had the same preference order, preferring glucose over xylose (Fig.…”

Section: Diauxic Lags Promote Complementarity Coexistence and Multistabilitymentioning

confidence: 99%

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confidence: 99%

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Complementary resource preferences spontaneously emerge in diauxic microbial communities

Wang

Goyal

Dubinkina

et al. 2021

Preprint

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“…The simultaneous and e cient bioconversion of the two sugars into ethanol are two of the prerequisites for large-scale production of cellulosic ethanol. However, due to carbon catabolite repression (CCR), a considerable amount of wild microbes and engineered microbes having exogenous xylose-metabolic pathways, like Zymomonas mobilis, Escherichia coli, Saccharomyces cerevisiae and Bacillus amyloliquefaciens, prefer to use glucose, and therefore their xylose utilization generally lags behind glucose utilization (2)(3)(4)(5). This greatly hampers the large-scale application of cellulosic ethanol in industry.…”

Section: Introductionmentioning

confidence: 99%

Cellulosic Ethanol Production by Engineered Consortia of Scheffersomyces Stipitis and Zymomonas Mobilis

Sun

Zhang

et al. 2021

Preprint

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Background: As one of the clean and sustainable energies, lignocellulosic ethanol has achieved much attention around the world. The production of lignocellulosic ethanol does not compete with people for food, while the consumption of ethanol could contribute to the carbon dioxide emission reduction. Two of the conditions that are needed to attain cost-efficient lignocellulosic ethanol production at an industrial scale are the simultaneous transformation of glucose and xylose to ethanol and a highly efficient ethanol fermentation process. Results: In this study, the consortia consisting of suspended Scheffersomyces stipitis CICC1960 and Zymomonas mobilis 8b were cultivated to successfully depress carbon catabolite repression (CCR) in 80G40XRM. With this strategy, a 5.52% more xylose consumption and a 6.52% higher ethanol titer were achieved by the consortium, in which the inoculation ratio between S. stipitis and Z. mobilis was 1:3, at the end of fermentation compared with the Z. mobilis 8b mono-fermentation. Subsequently, one copy of the xylose metabolic genes was inserted into the Z. mobilis 8b genome to construct Z. mobilis FR2, leading to the xylose final-consumption amount and ethanol titer improvement by 15.36% and 6.81%, respectively. Finally, various concentrations of corn stover hydrolysates, in which the sum of glucose and xylose concentrations in the hydrolysates were 60, 90, and 120 g/L respectively, were used to evaluate the fermentation performance of the consortium consisting of S. stipitis CICC1960 and Z. mobilis FR2. Fermentation results showed that a 1.56% - 4.59% higher ethanol titer was achieved by the consortium compared with the Z. mobilis FR2 mono-fermentation, and a 46.12% - 102.14% higher ethanol titer was observed in the consortium fermentation when compared with the S. stipitis CICC1960 mono-fermentation. Conclusions: The fermentation strategy used in this study, i.e., using a genetically modified consortium, had a superior performance in ethanol production, as compared with the S. stipitis CICC1960 mono-fermentation and the Z. mobilis FR2 mono-fermentation alone. Thus, this strategy has potential for future lignocellulosic ethanol production.

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Complementary resource preferences spontaneously emerge in diauxic microbial communities

et al. 2021

View full text Add to dashboard Cite

Many microbes grow diauxically, utilizing the available resources one at a time rather than simultaneously. The properties of communities of microbes growing diauxically remain poorly understood, largely due to a lack of theory and models of such communities. Here, we develop and study a minimal model of diauxic microbial communities assembling in a serially diluted culture. We find that unlike co-utilizing communities, diauxic community assembly repeatably and spontaneously leads to communities with complementary resource preferences, namely communities where species prefer different resources as their top choice. Simulations and theory explain that the emergence of complementarity is driven by the disproportionate contribution of the top choice resource to the growth of a diauxic species. Additionally, we develop a geometric approach for analyzing serially diluted communities, with or without diauxie, which intuitively explains several additional emergent community properties, such as the apparent lack of species which grow fastest on a resource other than their most preferred resource. Overall, our work provides testable predictions for the assembly of natural as well as synthetic communities of diauxically shifting microbes.

show abstract

Availability of the Molecular Switch XylR Controls Phenotypic Heterogeneity and Lag Duration during Escherichia coli Adaptation from Glucose to Xylose

Cited by 9 publications

References 64 publications

Complementary resource preferences spontaneously emerge in diauxic microbial communities

Complementary resource preferences spontaneously emerge in diauxic microbial communities

Cellulosic Ethanol Production by Engineered Consortia of Scheffersomyces Stipitis and Zymomonas Mobilis

Complementary resource preferences spontaneously emerge in diauxic microbial communities

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