Rethinking the Hierarchy of Sugar Utilization in Bacteria

Beisel, Chase L.; Afroz, Taliman

doi:10.1128/jb.00890-15

Cited by 30 publications

(26 citation statements)

References 27 publications

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“…However, carbon catabolite repression (CCR) inhibits hosts from consuming diverse substrates simultaneously (i.e., E. coli mainly consumes glucose first in a glucose/xylose medium). The CCR is often explained by glucose inhibition on the synthesis of enzymes involved in catabolism of other carbon sources, while recent studies suggest that the presence of subpopulations within E. coli cultures can have different carbon utilization hierarchies [ 18 , 19 ]. To investigate glucose catabolite repression, we grew the strains with a mixed carbon source of 10 g/L of glucose and 6 g/L of xylose, and measured the consumption of the two sugars (Fig.…”

Section: Resultsmentioning

confidence: 99%

Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants

Hollinshead

Rodrı́guez

Martín

et al. 2016

Biotechnol Biofuels

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BackgroundGlycolysis breakdowns glucose into essential building blocks and ATP/NAD(P)H for the cell, occupying a central role in its growth and bio-production. Among glycolytic pathways, the Entner Doudoroff pathway (EDP) is a more thermodynamically favorable pathway with fewer enzymatic steps than either the Embden–Meyerhof–Parnas pathway (EMPP) or the oxidative pentose phosphate pathway (OPPP). However, Escherichia coli do not use their native EDP for glucose metabolism.ResultsOverexpression of edd and eda in E. coli to enhance EDP activity resulted in only a small shift in the flux directed through the EDP (~20 % of glycolysis flux). Disrupting the EMPP by phosphofructokinase I (pfkA) knockout increased flux through OPPP (~60 % of glycolysis flux) and the native EDP (~14 % of glycolysis flux), while overexpressing edd and eda in this ΔpfkA mutant directed ~70 % of glycolytic flux through the EDP. The downregulation of EMPP via the pfkA deletion significantly decreased the growth rate, while EDP overexpression in the ΔpfkA mutant failed to improve its growth rates due to metabolic burden. However, the reorganization of E. coli glycolytic strategies did reduce glucose catabolite repression. The ΔpfkA mutant in glucose medium was able to cometabolize acetate via the citric acid cycle and gluconeogenesis, while EDP overexpression in the ΔpfkA mutant repressed acetate flux toward gluconeogenesis. Moreover, 13C-pulse experiments in the ΔpfkA mutants showed unsequential labeling dynamics in glycolysis intermediates, possibly suggesting metabolite channeling (metabolites in glycolysis are pass from enzyme to enzyme without fully equilibrating within the cytosol medium).ConclusionsWe engineered E. coli to redistribute its native glycolytic flux. The replacement of EMPP by EDP did not improve E. coli glucose utilization or biomass growth, but alleviated catabolite repression. More importantly, our results supported the hypothesis of channeling in the glycolytic pathways, a potentially overlooked mechanism for regulating glucose catabolism and coutilization of other substrates. The presence of channeling in native pathways, if proven true, would affect synthetic biology applications and metabolic modeling.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0630-y) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants

Hollinshead

Rodrı́guez

Martín

et al. 2016

Biotechnol Biofuels

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“…consuming different sugars, as this has been observed in other bacteria and may play a role in clostridia (31,37,38).…”

Section: Discussionmentioning

confidence: 63%

Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in Clostridium acetobutylicum ATCC 824

et al. 2018

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Bacterial fermentation of carbohydrates from sustainable lignocellulosic biomass into commodity chemicals by the anaerobic bacteriumClostridium acetobutylicumis a promising alternative source to fossil fuel-derived chemicals. Recently, it was demonstrated that xylose is not appreciably fermented in the presence of arabinose, revealing a hierarchy of pentose utilization in this organism (L. Aristilde, I. A. Lewis, J. O. Park, and J. D. Rabinowitz, Appl Environ Microbiol 81:1452–1462, 2015,https://doi.org/10.1128/AEM.03199-14). The goal of the current study is to characterize the transcriptional regulation that occurs and perhaps drives this pentose hierarchy. Carbohydrate consumption rates showed that arabinose, like glucose, actively represses xylose utilization in cultures fermenting xylose. Further, arabinose addition to xylose cultures led to increased acetate-to-butyrate ratios, which indicated a transition of pentose catabolism from the pentose phosphate pathway to the phosphoketolase pathway. Transcriptome sequencing (RNA-Seq) confirmed that arabinose addition to cells actively growing on xylose resulted in increased phosphoketolase (CA_C1343) mRNA levels, providing additional evidence that arabinose induces this metabolic switch. A significant overlap in differentially regulated genes after addition of arabinose or glucose suggested a common regulation mechanism. A putative open reading frame (ORF) encoding a potential catabolite repression phosphocarrier histidine protein (Crh) was identified that likely participates in the observed transcriptional regulation. These results substantiate the claim that arabinose is utilized preferentially over xylose inC. acetobutylicumand suggest that arabinose can activate carbon catabolite repression via Crh. Furthermore, they provide valuable insights into potential mechanisms for altering pentose utilization to modulate fermentation products for chemical production.IMPORTANCEClostridium acetobutylicumcan ferment a wide variety of carbohydrates to the commodity chemicals acetone, butanol, and ethanol. Recent advances in genetic engineering have expanded the chemical production repertoire ofC. acetobutylicumusing synthetic biology. Due to its natural properties and genetic engineering potential, this organism is a promising candidate for converting biomass-derived feedstocks containing carbohydrate mixtures to commodity chemicals via natural or engineered pathways. Understanding how this organism regulates its metabolism during growth on carbohydrate mixtures is imperative to enable control of synthetic gene circuits in order to optimize chemical production. The work presented here unveils a novel mechanism via transcriptional regulation by a predicted Crh that controls the hierarchy of carbohydrate utilization and is essential for guiding robust genetic engineering strategies for chemical production.

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“…How do the timescales of signal fluctuations shape the design of sensors and regulatory control? Many reviews summarize current knowledge of preferential resource use in bacteria (Beisel & Afroz, ; Chubukov, Gerosa, Kochanowski, & Sauer, ; Deutscher, ; Görke & Stülke, ).…”

Section: Glycansmentioning

confidence: 99%

Receptor uptake arrays for vitamin B₁₂, siderophores, and glycans shape bacterial communities

Frank

2017

Ecology and Evolution

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Molecular variants of vitamin B12, siderophores, and glycans occur. To take up variant forms, bacteria may express an array of receptors. The gut microbe Bacteroides thetaiotaomicron has three different receptors to take up variants of vitamin B12 and 88 receptors to take up various glycans. The design of receptor arrays reflects key processes that shape cellular evolution. Competition may focus each species on a subset of the available nutrient diversity. Some gut bacteria can take up only a narrow range of carbohydrates, whereas species such as B. thetaiotaomicron can digest many different complex glycans. Comparison of different nutrients, habitats, and genomes provides opportunity to test hypotheses about the breadth of receptor arrays. Another important process concerns fluctuations in nutrient availability. Such fluctuations enhance the value of cellular sensors, which gain information about environmental availability and adjust receptor deployment. Bacteria often adjust receptor expression in response to fluctuations of particular carbohydrate food sources. Some species may adjust expression of uptake receptors for specific siderophores. How do cells use sensor information to control the response to fluctuations? This question about regulatory wiring relates to problems that arise in control theory and artificial intelligence. Control theory clarifies how to analyze environmental fluctuations in relation to the design of sensors and response systems. Recent advances in deep learning studies of artificial intelligence focus on the architecture of regulatory wiring and the ways in which complex control networks represent and classify environmental states. I emphasize the similar design problems that arise in cellular evolution, control theory, and artificial intelligence. I connect those broad conceptual aspects to many testable hypotheses for bacterial uptake of vitamin B12, siderophores, and glycans.

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Rethinking the Hierarchy of Sugar Utilization in Bacteria

Cited by 30 publications

References 27 publications

Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants

Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants

Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in Clostridium acetobutylicum ATCC 824

Receptor uptake arrays for vitamin B₁₂, siderophores, and glycans shape bacterial communities

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Rethinking the Hierarchy of Sugar Utilization in Bacteria

Cited by 30 publications

References 27 publications

Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants

Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants

Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in Clostridium acetobutylicum ATCC 824

Receptor uptake arrays for vitamin B12, siderophores, and glycans shape bacterial communities

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Receptor uptake arrays for vitamin B₁₂, siderophores, and glycans shape bacterial communities