Metabolic Detoxification of 2-Oxobutyrate by Remodeling Escherichia coli Acetate Bypass

Fang, Yu; Zhang, Shuyan; Wang, Jianli; Yin, Lianghong; Zhang, Hailing; Wang, Zhen; Song, Jie; Hu, Xiaoqing

doi:10.3390/metabo11010030

Cited by 9 publications

(9 citation statements)

References 45 publications

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“…As expected, we observed a decrease in 2-aminobutyrate and an increase in 2KB compared to that of SYN12 ( Figure 3B ). Because 2KB is directly upstream of 1-propanol, the decrease in 1-propanol titer is counterintuitive, and may be a result of 2KB toxicity ( Zhang et al, 2016 ; Fang et al, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

“…As an indispensable metabolic intermediate in biological metabolism, 2-KB is found in the biosynthesis of L-isoleucine ( Park et al, 2012 ; Yin et al, 2012 ), 2-aminobutyrate ( Xu et al, 2019 ), 1-butanol ( Atsumi and Liao, 2008 ), L-homoalanine ( Zhang et al, 2010 ), and so on. However, because of its structural similarity with pyruvate, 2KB competitively inhibits enzymes used in pyruvate metabolism at high concentrations, which causes cellular toxicity ( Zhang et al, 2016 ; Fang et al, 2021 ). As such, this suggests that enhancing the turnover rate of 2-KB to 1-propanol with KivD and YqhD may relieve toxicity caused by 2KB accumulation.…”

Section: Discussionmentioning

confidence: 99%

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Metabolomics-Driven Identification of the Rate-Limiting Steps in 1-Propanol Production

et al. 2022

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The concerted effort for bioproduction of higher alcohols and other commodity chemicals has yielded a consortium of metabolic engineering techniques to identify targets to enhance performance of engineered microbial strains. Here, we demonstrate the use of metabolomics as a tool to systematically identify targets for improved production phenotypes in Escherichia coli. Gas chromatography/mass spectrometry (GC/MS) and ion-pair LC-MS/MS were performed to investigate metabolic perturbations in various 1-propanol producing strains. Two initial strains were compared that differ in the expression of the citramalate and threonine pathways, which hold a synergistic relationship to maximize production yields. While this results in increased productivity, no change in titer was observed when the threonine pathway was overexpressed beyond native levels. Metabolomics revealed accumulation of upstream byproducts, norvaline and 2-aminobutyrate, both of which are derived from 2-ketobutyrate (2KB). Eliminating the competing pathway by gene knockouts or improving flux through overexpression of glycolysis gene effectively increased the intracellular 2KB pool. However, the increase in 2KB intracellular concentration yielded decreased production titers, indicating toxicity caused by 2KB and an insufficient turnover rate of 2KB to 1-propanol. Optimization of alcohol dehydrogenase YqhD activity using an ribosome binding site (RBS) library improved 1-propanol titer (g/L) and yield (g/g of glucose) by 38 and 29% in 72 h compared to the base strain, respectively. This study demonstrates the use of metabolomics as a powerful tool to aid systematic strain improvement for metabolically engineered organisms.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Metabolomics-Driven Identification of the Rate-Limiting Steps in 1-Propanol Production

et al. 2022

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“…Up-regulation of four genes involved in threonine biosynthesis from L-aspartate, hom, thrB, thrC , and thrD , may involve enhanced threonine biosynthesis in MRSA under NaP treatment. Synthesized threonine can then be converted into glycine and serine and, subsequently, pyruvate for energy or into isoleucine ( Fang et al, 2021 ). During the conversion, ilvA is responsible for conversion of serine to pyruvate and, together with sdaAB , the conversion of threonine into 2-oxobutyrate (2-OBA), a precursor metabolite of isoleucine.…”

Section: Discussionmentioning

confidence: 99%

“…However, NaP did not affect the gene expression of enzymes involved in conversion of threonine into glycine or of glycine into serine, suggesting that NaP-induced ilvA expression is involved in 2-OBA generation. Of note, 2-OBA is a toxic metabolic intermediate leading to the arrest of cell growth in most microorganisms ( LaRossa et al, 1987 ; Fang et al, 2021 ). Thus, NaP-induced ilvA expression following up-regulated threonine biosynthesis may suppress MRSA growth by excessive 2-OBA production.…”

Section: Discussionmentioning

confidence: 99%

RNA-Seq-based transcriptome analysis of methicillin-resistant Staphylococcus aureus growth inhibition by propionate

Lee

Park

et al. 2022

Front. Microbiol.

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Staphylococcus aureus is a pathogen that causes a variety of infectious diseases such as pneumonia, endocarditis, and septic shock. Methicillin-resistant S. aureus (MRSA) evades virtually all available treatments, creating the need for an alternative control strategy. Although we previously demonstrated the inhibitory effect of sodium propionate (NaP) on MRSA, the regulatory mechanism of this effect remains unclear. In this study, we investigated the regulatory mechanism responsible for the inhibitory effect of NaP on MRSA using RNA-Seq analysis. Total RNAs were isolated from non-treated and 50 mM NaP-treated S. aureus USA300 for 3 h and transcriptional profiling was conducted by RNA-Seq analysis. A total of 171 differentially expressed genes (DEGs) with log2 fold change ≥2 and p < 0.05 was identified in the NaP treatment group compared with the control group. Among the 171 genes, 131 were up-regulated and 40 were down-regulated. Upon gene ontology (GO) annotation analysis, total 26 specific GO terms in “Biological process,” “Molecular function,” and “Cellular component” were identified in MRSA treated with NaP for 3 h. “Purine metabolism”; “riboflavin metabolism”; and “glycine, serine, and threonine metabolism” were identified as major altered metabolic pathways among the eight significantly enriched KEGG pathways in MRSA treated with NaP. Furthermore, the MRSA strains deficient in purF, ilvA, ribE, or ribA, which were the up-regulated DEGs in the metabolic pathways, were more susceptible to NaP than wild-type MRSA. Collectively, these results demonstrate that NaP attenuates MRSA growth by altering its metabolic pathways, suggesting that NaP can be used as a potential bacteriostatic agent for prevention of MRSA infection.

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“…In our study, the results of both transcriptome and metabolome analyses showed that propanoate metabolism pathways were induced by sewage treatment and key genes related to propanoate metabolism (Table S5). Furthermore, the downregulated metabolite was 2-oxobutanoate (2-OBA), which as a toxic metabolic intermediate, generally arrests the cell growth of most microorganisms and blocks the biosynthesis of target metabolites [35-36]. In the wastewater treatment process, the metabolite of 2-OBA is downregulated, which can promote the effect of microalgae on wastewater treatment and maintain the normal metabolism of microalgae.…”

Section: Discussionmentioning

confidence: 99%

Combined transcriptome and metabolome analysis of a new species of microalgae from Tibetan plateau and its response to sewage treatment

Wang

Zhang

Chen

et al. 2022

Preprint

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Microalgae are pivotal in maintaining water quality in the lakes and rivers of Qinghai-Tibet plateau. The optimum sewage treatment conditions for Desmodesmus sp. are, temperature: 20–25°C, light intensity: 3000–8000 lx, and pH: 7.0–7.5, identified based on orthogonal experiments. The maximum removal rate of total nitrogen, total phosphorus, and chemical oxygen demand was more than 95% in the actual sewage treatment. The sewage treatment capacity of Desmodesmus sp. from plateau is higher than that from plains under the same treatment conditions. To identify the differentially expressed genes and metabolites in Desmodesmus sp. in response to sewage treatment, a combination of metabolomics and transcriptomics was employed to the microalgae with and without sewage treatment. The results showed that the oxidative phosphorylation, photosynthesis, and propanoate metabolism pathways were the most significantly enriched pathways in sewage treatment. Further, the metabolism of adenosine diphosphate, 2-oxobutanoate, and succinate were significantly upregulated, downregulated, and both upregulated and downregulated, respectively, as shown by the combined transcriptome and metabolome analysis. Additionally, we found that sewage treatment could also induce numerous changes in the primary metabolism, such as carbohydrate, fatty acid biosynthesis, and amino acid metabolism when compared with control. Overall, our results should improve fundamental knowledge of molecular responses to Desmodesmus sp. in sewage treatment and contribute to the design of strategies in microalgae response to sewage treatment.

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Metabolic Detoxification of 2-Oxobutyrate by Remodeling Escherichia coli Acetate Bypass

Cited by 9 publications

References 45 publications

Metabolomics-Driven Identification of the Rate-Limiting Steps in 1-Propanol Production

Metabolomics-Driven Identification of the Rate-Limiting Steps in 1-Propanol Production

RNA-Seq-based transcriptome analysis of methicillin-resistant Staphylococcus aureus growth inhibition by propionate

Combined transcriptome and metabolome analysis of a new species of microalgae from Tibetan plateau and its response to sewage treatment

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