Advances in the optimization of central carbon metabolism in metabolic engineering

Wu, Zhenke; Liang, Xiqin; Li, Mingkai; Ma, Mengyu; Zheng, Qin; Li, Defang; An, Tianyue; Wang, Guoli

doi:10.1186/s12934-023-02090-6

Cited by 22 publications

(10 citation statements)

References 87 publications

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“…Central carbon metabolism, which includes glycolysis, pentose phosphate pathway (PPP) and tricarboxylic acid cycle (TCA), is required for bacteria to generate energy in the form of ATP. This process provides precursors for all the biosynthetic reactions that are required for cell survival [66, 67]. This makes central carbon metabolism i.e., carbon uptake and carbon utilization, an attractive antimicrobial target because these processes are typically essential for microbial survival [68–70].…”

Section: Resultsmentioning

confidence: 99%

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Providing insight into the mechanism of action of Cationic Lipidated Oligomers (CLOs) using metabolomics

Hussein,

Mahboob,

Tait

et al. 2024

Preprint

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The increasing resistance of clinically relevant microbes against current commercially available antimicrobials underpins the urgent need for alternative and novel treatment strategies. Cationic lipidated oligomers (CLOs) are innovative alternatives to antimicrobial peptides, and have reported antimicrobial potential. An understanding of their antimicrobial mechanism of action is required to rationally design future treatment strategies for CLOs, either in monotherapy or synergistic combinations. In the present study, metabolomics was used to investigate the potential metabolic pathways involved in the mechanisms of antibacterial activity of one CLO, C12-o-(BG-D)-10, which we have previously shown to be effective against methicillin-resistantStaphylococcus aureus(MRSA) ATCC 43300. The metabolomes of MRSA ATCC 43300 at 1, 3 and 6 h following treatment with C12-o-(BG-D)-10 (48 µg/mL i.e., 3x MIC) were compared to those of the untreated controls.Our findings reveal that the studied CLO, C12-o-(BG-D)-10, disorganized the bacterial membrane as the first step towards its antimicrobial effect, as evidenced by marked perturbations in the bacterial membrane lipids and peptidoglycan biosynthesis observed at early time points i.e., 1, and 3 h. Central carbon metabolism, and biosynthesis of DNA, RNA, and arginine were also vigorously perturbed, mainly at early time points. Moreover, bacterial cells were under osmotic and oxidative stress across all time points, evident by perturbations of trehalose biosynthesis and pentose phosphate shunt. Overall, this metabolomics study has, for the first time, revealed that the antimicrobial action of C12-o-(BG-D)-10 may potentially stem from the dysregulation of multiple metabolic pathways.ImportanceAntimicrobial resistance poses a significant challenge to healthcare systems worldwide. Novel anti-infective therapeutics are urgently needed to combat drug-resistant microorganisms. Cationic lipidated oligomers (CLOs) show promise as new antibacterial agents against Gram-positive pathogens likeStaphylococcus aureus(MRSA). Understanding their molecular mechanism(s) of antimicrobial action may help design synergistic CLO treatments along with monotherapy. Here, we describe the first metabolomics study to investigate the killing mechanism(s) of CLOs against MRSA. The results of our study indicate that the CLO, C12-o-(BG-D)-10, had a notable impact on the biosynthesis and organization of the bacterial cell envelope. C12-o-(BG-D)-10 also inhibits arginine, histidine, central carbon metabolism, and trehalose production, adding to its antibacterial characteristics. This work illuminates the unique mechanism of action of C12-o-(BG-D)-10 and opens an avenue to design innovative antibacterial oligomers/polymers for future clinical applications.

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Section: Resultsmentioning

confidence: 99%

“…This process provides precursors for all the biosynthetic reactions that are required for cell survival [66,67]. This makes central carbon metabolism i.e., carbon uptake and carbon utilization, an attractive antimicrobial target because these processes are typically essential for microbial survival [68][69][70].…”

Section: Central Carbon Metabolismmentioning

confidence: 99%

Providing insight into the mechanism of action of Cationic Lipidated Oligomers (CLOs) using metabolomics

Hussein,

Mahboob,

Tait

et al. 2024

Preprint

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“…coli, glucose transport first passes through a phosphoenolpyruvate-dependent phosphatase transfer system (PTS), which requires significant consumption of PEP . PEP also serves as an important precursor for hydroxytyrosol synthesis . Thus, the PTS system was inactivated to enhance the supply of PEP.…”

Section: Resultsmentioning

confidence: 99%

“…28 PEP also serves as an important precursor for hydroxytyrosol synthesis. 29 Thus, the PTS system was inactivated to enhance the supply of PEP. Strain HJ3 was obtained by knocking out ptsG and crr in strain HJ2, and the titer of hydroxytyrosol reached 1.10 g/L at 48 h. Considering that the presence of the phenylalanine synthesis branch would only reduce the flux to hydroxytyrosol, strain HJ4 was generated by knocking out pheA in HJ3 to achieve a maximum hydroxytyrosol titer of 1.43 g/L for 72 h. Finally, ADH6 from S. cerevisiae was overexpressed to enhance the efficiency of the dehydrogenation.…”

Section: Construction Of the Hydroxytyrosol Biosynthetic Pathwaymentioning

confidence: 99%

Promoting FADH₂ Regeneration of Hydroxylation for High-Level Production of Hydroxytyrosol from Glycerol in Escherichia coli

Wang,

Chen

et al. 2023

J. Agric. Food Chem.

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Hydroxytyrosol is a natural polyphenolic compound widely used in the food and drug industries. The current commercial production of hydroxytyrosol relies mainly on plant extracts, which involve long extraction cycles and various raw materials. Microbial fermentation has potential value as an environmentally friendly and low-cost method. Here, a de novo biosynthetic pathway of hydroxytyrosol has been designed and constructed in an Escherichia coli strain with released tyrosine feedback inhibition. By introduction of hpaBC from E. coli and ARO10 and ADH6 from Saccharomyces cerevisiae, the de novo biosynthesis of hydroxytyrosol was achieved. An important finding in cofactor engineering is that the introduction of L-amino acid deaminase (LAAD) promotes not only cofactor regeneration but also metabolic flow redistribution. To further enhance the hydroxylation process, different 4-hydroxyphenylacetate 3-monooxygenase (hpaB) mutants and HpaBC proteins from different sources were screened. Finally, after optimization of the carbon source, pH, and seed medium, the optimum engineered strain produced 9.87 g/L hydroxytyrosol in a 5 L bioreactor. This represents the highest titer reported to date for de novo biosynthesis of hydroxytyrosol in microorganisms.

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“…cerevisiae. Since the resulting strains can accumulate different carbon metabolites, including CO 2 fixation products such as pyruvate (see above), they might provide suitable hosts to put related biosensor systems to the test. ,, …”

Section: Identification Of Novel Biosensor Systems and Contextualizat...mentioning

confidence: 99%

In Vivo Detection of Low Molecular Weight Platform Chemicals and Environmental Contaminants by Genetically Encoded Biosensors

et al. 2023

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Genetically encoded biosensor systems operating in living cells are versatile, cheap, and transferable tools for the detection and quantification of a broad range of small molecules. This review presents state-of-the-art biosensor designs and assemblies, featuring transcription factor-, riboswitch-, and enzyme-coupled devices, highly engineered fluorescent probes, and emerging two-component systems. Importantly, (bioinformaticassisted) strategies to resolve contextual issues, which cause biosensors to miss performance criteria in vivo, are highlighted. The optimized biosensing circuits can be used to monitor chemicals of low molecular mass (<200 g mol −1 ) and physicochemical properties that challenge conventional chromatographical methods with high sensitivity. Examples herein include but are not limited to formaldehyde, formate, and pyruvate as immediate products from (synthetic) pathways for the fixation of carbon dioxide (CO 2 ), industrially important derivatives like small-and medium-chain fatty acids and biofuels, as well as environmental toxins such as heavy metals or reactive oxygen and nitrogen species. Lastly, this review showcases biosensors capable of assessing the biosynthesis of platform chemicals from renewable resources, the enzymatic degradation of plastic waste, or the bioadsorption of highly toxic chemicals from the environment. These applications offer new biosensor-based manufacturing, recycling, and remediation strategies to tackle current and future environmental and socioeconomic challenges including the wastage of fossil fuels, the emission of greenhouse gases like CO 2 , and the pollution imposed on ecosystems and human health.

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Advances in the optimization of central carbon metabolism in metabolic engineering

Cited by 22 publications

References 87 publications

Providing insight into the mechanism of action of Cationic Lipidated Oligomers (CLOs) using metabolomics

Providing insight into the mechanism of action of Cationic Lipidated Oligomers (CLOs) using metabolomics

Promoting FADH₂ Regeneration of Hydroxylation for High-Level Production of Hydroxytyrosol from Glycerol in Escherichia coli

In Vivo Detection of Low Molecular Weight Platform Chemicals and Environmental Contaminants by Genetically Encoded Biosensors

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Advances in the optimization of central carbon metabolism in metabolic engineering

Cited by 22 publications

References 87 publications

Providing insight into the mechanism of action of Cationic Lipidated Oligomers (CLOs) using metabolomics

Providing insight into the mechanism of action of Cationic Lipidated Oligomers (CLOs) using metabolomics

Promoting FADH2 Regeneration of Hydroxylation for High-Level Production of Hydroxytyrosol from Glycerol in Escherichia coli

In Vivo Detection of Low Molecular Weight Platform Chemicals and Environmental Contaminants by Genetically Encoded Biosensors

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Promoting FADH₂ Regeneration of Hydroxylation for High-Level Production of Hydroxytyrosol from Glycerol in Escherichia coli