Inhibition of glycine cleavage system by pyridoxine 5′‐phosphate causes synthetic lethality in glyA yggS and serA yggS in Escherichia coli

Ito, Tomokazu; Hori, Ran; Hemmi, Hisashi; Downs, Diana M.; Yoshimura, Teizo

doi:10.1111/mmi.14415

Cited by 21 publications

(26 citation statements)

References 61 publications

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“…A previous study showed that attenuation of glyA transcription resulted in increased L-Ser accumulation, a decrease in the purine pool, poor growth and cell elongation ( Fig S1, Additional le 1) [25,26]. The same phenomenon was observed in this study; SSW-02 cells were elongated and exhibited unstable growth at the early stage of fermentation.…”

Section: In Uence Of Mutations In Glya On L-serine Production and Celsupporting

confidence: 88%

Rational Metabolic Engineering of Escherichia Coli for High-yield L-serine Production

Wang¹,

Wu²,

Wang³

et al. 2020

Preprint

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Background: L-serine is widely used in the food, cosmetic and pharmaceutical industries, and direct fermentation of L-serine from glucose is an attractive technique. However, L-serine producers have historically been developed via classical random mutagenesis due to the complicated metabolic network and regulatory mechanism of L-serine production, leading to un-optimal productivity and yield of L-serine and thus limiting its large-scale industrial production. Result: In this study, a high-yield and high-productivity Escherichia coli strain was constructed by a defined genetic modification methodology for L-serine production. First, L-serine-mediated feedback inhibition was removed and L-serine biosynthetic pathway genes (serAfr, serC and serB) associated with phosphoglycerate kinase (pgk) were overexpressed. Secondly, L-serine conversion pathway was further examined by introducing a glyA mutation (K229G) and deleting other degrading enzymes based on deletion of initial sdaA. Finally, the L-serine transport system was rationally engineered to reduce the uptake and accelerate the export of L-serine. The optimally engineered strain produced 35 g/L L-serine with a productivity of 0.98 g/L/h and yield of 0.42 g/g glucose in a 5-L fermenter, the highest productivity and yield of L-serine from glucose reported to date. Transcriptome and intermediate metabolite were analyzed to further understand the regulatory mechanism of L-serine production. Conclusion: These results demonstrated that combined metabolic and bioprocess engineering strategies can improve L-serine productivity and yield, thus providing basic principles for rationally designing of high-yield production strains and paving the way for towards a simple and economical process for industrial L-serine production.

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Section: In Uence Of Mutations In Glya On L-serine Production and Celsupporting

confidence: 88%

Rational Metabolic Engineering of Escherichia Coli for High-yield L-serine Production

Wang¹,

Wu²,

Wang³

et al. 2020

Preprint

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“…The culture medium was deproteinized with HClO 4 (a final concentration of 0.9 M), neutralized by K 2 CO 3 , and clarified by centrifugation. The B 6 vitamers were separated with an octadecylsilyl (ODS) column (Cosmosil AR-II; Nacalai Tesque) (250 mm by 4.6 mm, 5-m particle size) using a gradient program as described previously (17,18). The flow rate was 1.0 ml per min, and the excitation and emission wavelengths were 328 nm and 393 nm, respectively.…”

Section: Methodsmentioning

confidence: 99%

“…During the study of the biosynthesis, homeostasis, and metabolic network of vitamin B 6 in Escherichia coli and Salmonella enterica (16)(17)(18), we found that E. coli strains lacking pdxJ had different PL requirements than those lacking pdxH. This result was unexpected given that both lesions abolish PLP biosynthesis.…”

mentioning

confidence: 91%

Pyridoxal Reductase, PdxI, Is Critical for Salvage of Pyridoxal in Escherichia coli

Ito

Downs

2020

J Bacteriol

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Pyridoxal 5′-phosphate (PLP) is the biologically active form of vitamin B6 and an essential cofactor in all organisms. In Escherichia coli, PLP is synthesized via the deoxyxylulose 5-phosphate (DXP)-dependent pathway that includes seven enzymatic steps and generates pyridoxine 5′-phosphate as an intermediate. Additionally, E. coli is able to salvage pyridoxal, pyridoxine, and pyridoxamine B6 vitamers to produce PLP using kinases PdxK/PdxY and pyridox(am)ine phosphate oxidase (PdxH). We found that E. coli strains blocked in PLP synthesis prior to the formation of pyridoxine 5′-phosphate (PNP) required significantly less exogenous pyridoxal (PL) than strains lacking pdxH and identified the conversion of PL to pyridoxine (PN) during cultivation to be the cause. Our data showed that PdxI, shown to have PL reductase activity in vitro, was required for the efficient salvage of PL in E. coli. The pdxI+ E. coli strains converted exogenous PL to PN during growth, while pdxI mutants did not. In total, the data herein demonstrated that PdxI is a critical enzyme in the salvage of PL by E. coli. IMPORTANCE The biosynthetic pathway of pyridoxal 5′-phosphate (PLP) has extensively been studied in Escherichia coli, yet limited information is available about the vitamin B6 salvage pathway. We show that the protein PdxI (YdbC) is the primary pyridoxal (PL) reductase in E. coli and is involved in the salvage of PL. The orthologs of PdxI occur in a wide range of bacteria and plants, suggesting that PL reductase in the B6 salvage pathway is more widely distributed than previously expected.

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“…Synthetic lethality between PLPBP and PLP holoenzymes, previously reported for E. coli yggS and either glyA [69,70] or serA [71], has also been found between pipY and cysK, the two most abundant PLP-binding proteins in S. elongatus [30]. Synthetic lethality probably reflects the common involvement of the corresponding protein pairs in amino acid and PLP homeostasis, but may also indicate that any relatively abundant PLP-binding protein could fulfill a role as a PLP reservoir, thus helping to cope with PLP toxicity.…”

Section: Common Structural and Functional Features Between Pipy And Omentioning

confidence: 82%

Distinctive Features of PipX, a Unique Signaling Protein of Cyanobacteria

Labella

Cantos

Salinas

et al. 2020

Life

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PipX is a unique cyanobacterial protein identified by its ability to bind to PII and NtcA, two key regulators involved in the integration of signals of the nitrogen/carbon and energy status, with a tremendous impact on nitrogen assimilation and gene expression in cyanobacteria. PipX provides a mechanistic link between PII, the most widely distributed signaling protein, and NtcA, a global transcriptional regulator of cyanobacteria. PII, required for cell survival unless PipX is inactivated or down-regulated, functions by protein–protein interactions with transcriptional regulators, transporters, and enzymes. In addition, PipX appears to be involved in a wider signaling network, supported by the following observations: (i) PII–PipX complexes interact with PlmA, an as yet poorly characterized transcriptional regulator also restricted to cyanobacteria; (ii) the pipX gene is functionally connected with pipY, a gene encoding a universally conserved pyridoxal phosphate binding protein (PLPBP) involved in vitamin B6 and amino acid homeostasis, whose loss-of-function mutations cause B6-dependent epilepsy in humans, and (iii) pipX is part of a relatively robust, six-node synteny network that includes pipY and four additional genes that might also be functionally connected with pipX. In this overview, we propose that the study of the protein–protein interaction and synteny networks involving PipX would contribute to understanding the peculiarities and idiosyncrasy of signaling pathways that are conserved in cyanobacteria.

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Inhibition of glycine cleavage system by pyridoxine 5′‐phosphate causes synthetic lethality in glyA yggS and serA yggS in Escherichia coli

Cited by 21 publications

References 61 publications

Rational Metabolic Engineering of Escherichia Coli for High-yield L-serine Production

Rational Metabolic Engineering of Escherichia Coli for High-yield L-serine Production

Pyridoxal Reductase, PdxI, Is Critical for Salvage of Pyridoxal in Escherichia coli

Distinctive Features of PipX, a Unique Signaling Protein of Cyanobacteria

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