A comparative study on the genomes, transcriptomes, and metabolic properties of Escherichia coli strains Nissle 1917, BL21(DE3), and MG1655

Zhao, Linlin; Yin, Guobin; Zhang, Yonglin; Duan, Chaofan; Wang, Yang; Kang, Zhen

doi:10.1016/j.engmic.2022.100012

Cited by 16 publications

(17 citation statements)

References 55 publications

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“…E. coli B and K‐12 strains differ in many aspects that are known to affect C. elegans phenotypes (Daegelen et al , 2009; Jeong et al , 2009; Studier et al , 2009; Maier et al , 2010; Reinke et al , 2010; Pinske et al , 2011; Yoon et al , 2012; Yen & Curran, 2016; Heestand et al , 2018; Neve et al , 2020; Stuhr & Curran, 2020; Zhao et al , 2022). Especially, K‐12 strains have longer lipopolysaccharides (LPS) in their cell wall than the B strains and the longer LPS of E. coli K‐12 strains trigger p38/PMK‐1 immune activation in C. elegans (Pradel et al , 1992; Aballay et al , 2003; Zhang et al , 2006; Maier et al , 2010; Leung et al , 2020; Ma et al , 2020).…”

Section: Resultsmentioning

confidence: 99%

Genome‐wide association and environmental suppression of the mortal germline phenotype of wild C. elegans

Frézal,

Saglio,

Zhang

et al. 2023

EMBO Reports

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The animal germline lineage needs to be maintained along generations. However, some Caenorhabditis elegans wild isolates display a mortal germline phenotype, leading to sterility after several generations at 25°C. Using a genome‐wide association approach, we detect a significant peak on chromosome III around 5 Mb, confirmed by introgressions. Thus, a seemingly deleterious genotype is maintained at intermediate frequency in the species. Environmental rescue is a likely explanation, and indeed associated bacteria and microsporidia suppress the phenotype of wild isolates as well as mutants in small RNA inheritance (nrde‐2) and histone modifications (set‐2). Escherichia coli strains of the K‐12 lineage suppress the phenotype compared to B strains. By shifting a wild strain from E. coli K‐12 to E. coli B, we find that memory of the suppressing condition is maintained over several generations. Thus, the mortal germline phenotype of wild C. elegans is in part revealed by laboratory conditions and may represent variation in epigenetic inheritance and environmental interactions. This study also points to the importance of non‐genetic memory in the face of environmental variation.

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Section: Resultsmentioning

confidence: 99%

Genome‐wide association and environmental suppression of the mortal germline phenotype of wild C. elegans

Frézal,

Saglio,

Zhang

et al. 2023

EMBO Reports

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“…JM109(DE3) reaction performance decreased with increasing formaldehyde concentration, but it still demonstrated higher initial rates and conversion rates than BL21(DE3) and ER2566. Genes involved in the glyoxylate shunt and tricarboxylic acid (TCA) cycle were up-regulated in the K strain as a result of analysing the transcriptomes of strains K and B in the previous study 28,29 . In BL21, however, both the glyoxylate shunt and the TCA cycle are activated.…”

Section: Catalytic Performance Of E Coli Deletion Variantsmentioning

confidence: 97%

Biotransformation pathway and side reaction engineering for the whole-cell production of glycolic acid from formaldehyde

Kim

et al. 2022

Preprint

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A very simple biocatalytic system for the synthesis of the industrially relevant C2 chemicals (e.g., glycolic acid (3)) from formaldehyde (1) was established by whole-cell biocatalyst. The biocatalytic system consisted of an engineered glyoxylate carboligase from Escherichia coli K-12 (EcGCL) and an aldehyde dehydrogenase (e.g., AldA from E. coli K-12). To improve glycolic acid production, we have investigated metabolic engineering to regulate substrate consumption and product bypass and E. coli-based strain optimization. The target compound was produced at rates of up to 20.3 U/g dry cells with conversions up to 92%. This study will ensure the sustainability of the green energy industry by synthesizing valuable C2 chemical from a single carbon compound, formaldehyde.

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“…Traditional probiotics can be easily engineered and are the chassis of choice. For example, engineered EcN has been developed into various biopharmaceuticals, − and its genomic, transcriptomic, and metabolic properties have been intensively studied . In fact, lactic acid bacteria now support various CRISPR/Cas systems − and have long been developed as mature heterologous production platforms, biocontrol systems, and biosensors .…”

Section: Chassismentioning

confidence: 99%

“…For example, engineered EcN has been developed into various biopharmaceuticals, 14−18 and its genomic, transcriptomic, and metabolic properties have been intensively studied. 86 In fact, lactic acid bacteria now support various CRISPR/Cas systems 87−91 and have long been developed as mature heterologous production platforms, 31 biocontrol systems, 76 and biosensors. 22 Meanwhile, Bif idobacterium are often used as an in situ delivery and production system for microfactories of various anticancer agents 13 and have been developed as a probiotic vaccine.…”

Section: Traditional Probiotic Chassismentioning

confidence: 99%

Intestinal Engineered Probiotics as Living Therapeutics: Chassis Selection, Colonization Enhancement, Gene Circuit Design, and Biocontainment

Huang

Lin

et al. 2022

ACS Synth. Biol.

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Intestinal probiotics are often used for the in situ treatment of diseases, such as metabolic disorders, tumors, and chronic inflammatory infections. Recently, there has been an increased emphasis on intelligent, customized treatments with a focus on long-term efficacy; however, traditional probiotic therapy has not kept up with this trend. The use of synthetic biology to construct gut-engineered probiotics as live therapeutics is a promising avenue in the treatment of specific diseases, such as phenylketonuria and inflammatory bowel disease. These studies generally involve a series of fundamental design issues: choosing an engineered chassis, improving the colonization ability of engineered probiotics, designing functional gene circuits, and ensuring the safety of engineered probiotics. In this review, we summarize the relevant past research, the progress of current research, and discuss the key issues that restrict the widespread application of intestinal engineered probiotic living therapeutics.

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A comparative study on the genomes, transcriptomes, and metabolic properties of Escherichia coli strains Nissle 1917, BL21(DE3), and MG1655

Cited by 16 publications

References 55 publications

Genome‐wide association and environmental suppression of the mortal germline phenotype of wild C. elegans

Genome‐wide association and environmental suppression of the mortal germline phenotype of wild C. elegans

Biotransformation pathway and side reaction engineering for the whole-cell production of glycolic acid from formaldehyde

Intestinal Engineered Probiotics as Living Therapeutics: Chassis Selection, Colonization Enhancement, Gene Circuit Design, and Biocontainment

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