Metabolic engineering of Escherichia coli for high-yield uridine production

Wu, Hongxia; Li, Yanjun; Ma, Qian; Li, Qiang; Jia, Zifan; Yang, Bo; Xu, Qingyang; Fan, Xiaoguang; Zhang, Chenglin; Chen, Ning; Xie, Xiulan

doi:10.1016/j.ymben.2018.09.001

Cited by 60 publications

(71 citation statements)

References 52 publications

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“…Second, CRISPR-Cas systems are versatile and can be used to transcriptionally repress or activate gene expression. CRISPRi and genome editing have been successfully applied in metabolic engineering to optimize gene expression levels for improved production of various molecules, including lycopene [ 117 ], isoprene [ 117 ], 4,4′-dihydroxybiphenyl (4HB) [ 118 ], malate [ 119 ], n-butanol [ 120 ], naringenin 7-sulfate [ 121 ], uridine [ 122 ], adipic acid [ 123 ], etc. Wu et al constructed the CRISPRi system to perturb the expression of multiple genes in the central metabolic pathway and achieved improved malonyl-CoA level by 223% [ 124 ].…”

Section: Applications Of Crispr-cas9/cas12a Biotechnology In Bacteriamentioning

confidence: 99%

CRISPR-Cas9/Cas12a biotechnology and application in bacteria

Yao

Liu

Jia

et al. 2018

Synthetic and Systems Biotechnology

112

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CRISPR-Cas technologies have greatly reshaped the biology field. In this review, we discuss the CRISPR-Cas with a particular focus on the associated technologies and applications of CRISPR-Cas9 and CRISPR-Cas12a, which have been most widely studied and used. We discuss the biological mechanisms of CRISPR-Cas as immune defense systems, recently-discovered anti-CRISPR-Cas systems, and the emerging Cas variants (such as xCas9 and Cas13) with unique characteristics. Then, we highlight various CRISPR-Cas biotechnologies, including nuclease-dependent genome editing, CRISPR gene regulation (including CRISPR interference/activation), DNA/RNA base editing, and nucleic acid detection. Last, we summarize up-to-date applications of the biotechnologies for synthetic biology and metabolic engineering in various bacterial species.

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Section: Applications Of Crispr-cas9/cas12a Biotechnology In Bacteriamentioning

confidence: 99%

CRISPR-Cas9/Cas12a biotechnology and application in bacteria

Yao

Liu

Jia

et al. 2018

Synthetic and Systems Biotechnology

112

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“…NupC and NupG were shown recently to be important ADP-glucose uptake transporters, and they are essential for the incorporation of extracellular ADP-glucose into glycogen during biosynthesis (16). The coordinate regulation of different purine/pyrimidine transporters is important for the utilization of nucleosides as carbon and nitrogen sources or nucleoside salvage under various starvation conditions (17).…”

Section: Resultsmentioning

confidence: 99%

“…The PurR regulon is essential for purine biosynthesis when salvage is limited. PurR repression is activated by the presence of hypoxanthine or guanine, signalling that the purine cytoplasmic concentration is su cient for growth (17,19,20). The inverse correlation for the modulation of mRNA levels for PurR-regulated purine biosynthetic genes and those of the ydhC and add genes (21) has been demonstrated during growth in minimal medium with glucose and adenine as a supplement, suggesting a role in purine salvage (11).…”

Section: Resultsmentioning

confidence: 99%

A novel transcription factor PunR and Nac are involved in purine and purine nucleoside transporter punC regulation in E. coli

Rodionova

Gao

Sastry

et al. 2021

Preprint

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Many genes in bacterial genomes are of unknown function, often referred to as y-genes. Recently, novel analytic methods have divided bacterial transcriptomes into independently modulated sets of genes (iModulons). Functionally annotated iModulons that contain y-genes lead to testable hypotheses to elucidate y-gene function. Inversely correlated expression of a putative transporter gene, ydhC, relative to purine biosynthetic genes, has led to the hypothesis that it encodes a purine-related transporter and revealed a LysR-family regulator, YdhB, with a predicted 23-bp palindromic binding motif. RNA-Seq analysis of a ydhB knockout mutant confirmed the YdhB-dependent activation of ydhC in the presence of adenosine. The deletion of either the ydhC or the ydhB gene led to a substantially decreased growth rate for E. coli in minimal medium with adenosine as the nitrogen source, as well as with inosine or guanosine. Taken together, we provide clear evidence that YdhB activates the expression of the ydhC gene that encodes a novel purine transporter in E. coli. We propose that the genes ydhB and ydhC be re-named as punR and punC, respectively.

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“…The yield of the product is an important indicator to evaluate the feasibility of microbial cell factories for industrial application (Hao et al, 2020; Wu et al, 2018). However, high‐yield production can be restricted by severe flux competition between central metabolism and the target synthetic pathway.…”

Section: Discussionmentioning

confidence: 99%

Flux redistribution of central carbon metabolism for efficient production of l‐tryptophan in Escherichia coli

Xiong

Zhu

Tian

et al. 2021

Biotech & Bioengineering

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Microbial production of l‐tryptophan (l‐trp) has received considerable attention because of its diverse applications in food additives and pharmaceuticals. Overexpression of rate‐limiting enzymes and blockage of competing pathways can effectively promote microbial production of l‐trp. However, the biosynthetic process remains suboptimal due to imbalanced flux distribution between central carbon and tryptophan metabolism, presenting a major challenge to further improvement of l‐trp yield. In this study, we redistributed central carbon metabolism to improve phosphoenolpyruvate (PEP) and erythrose‐4‐phosphate (E4P) pools in an l‐trp producing strain of Escherichia coli for efficient l‐trp synthesis. To do this, a phosphoketolase from Bifidobacterium adolescentis was introduced to strengthen E4P formation, and the l‐trp titer and yield increased to 10.8 g/L and 0.148 g/g glucose, respectively. Next, the phosphotransferase system was substituted with PEP‐independent glucose transport, meditated by a glucose facilitator from Zymomonas mobilis and native glucokinase. This modification improved l‐trp yield to 0.164 g/g glucose, concomitant with 58% and 40% decreases of acetate and lactate accumulation, respectively. Then, to channel more central carbon flux to the tryptophan biosynthetic pathway, several metabolic engineering strategies were applied to rewire the PEP‐pyruvate‐oxaloacetate node. Finally, the constructed strain SX11 produced 41.7 g/L l‐trp with an overall yield of 0.227 g/g glucose after 40 h fed‐batch fermentation in 5‐L bioreactor. This is the highest overall yield of l‐trp ever reported from a rationally engineered strain. Our results suggest the flux redistribution of central carbon metabolism to maintain sufficient supply of PEP and E4P is a promising strategy for efficient l‐trp biosynthesis, and this strategy would likely also increase the production of other aromatic amino acids and derivatives.

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Metabolic engineering of Escherichia coli for high-yield uridine production

Cited by 60 publications

References 52 publications

CRISPR-Cas9/Cas12a biotechnology and application in bacteria

CRISPR-Cas9/Cas12a biotechnology and application in bacteria

A novel transcription factor PunR and Nac are involved in purine and purine nucleoside transporter punC regulation in E. coli

Flux redistribution of central carbon metabolism for efficient production of l‐tryptophan in Escherichia coli

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