Rapid dissection of a complex phenotype through genomic-scale mapping of fitness altering genes

Warnecke, Tanya; Lynch, Michael; Karimpour-Fard, Anis; Lipscomb, Matthew L.; Handke, Paul; Mills, T; Ramey, Christopher Josh; Hoang, Thanh; Gill, Ryan T.

doi:10.1016/j.ymben.2009.12.002

Cited by 44 publications

(27 citation statements)

References 39 publications

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“…Five enzymes in superpathway of chorismate metabolism including AroF, TrpB, TrpC, TyrA and TyrB were upregulated under 3HP stress, in line with the previous study, 13 Chorismate is the principle common precursor of the aromatic amino acids tryptophan, tyrosine and phenylalanine, as well as the essential compounds tetrahydrofolate, ubiquinone-8, etc.…”

Section: Proteins Involved In Amino Acids Metabolismsupporting

confidence: 90%

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Development of a 3-hydroxypropionate resistantEscherichia colistrain

et al. 2016

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3-hydroxypropionate (3HP) is an important platform chemical, and its biosynthesis is severely restricted by the toxicity of 3HP on cell growth and survival. To improve Escherichia coli resistance to 3HP and reduce the total production cost in industrial applications, we have identified variations in protein expression level exposed to sub-lethal concentration of this chemical using 2-dimensional gel electrophoresis. Under 3HP stress, the amount of 46 proteins was increased while the amount of 23 proteins was reduced. According to the proteomic results, overexpression of some identified proteins significantly increased the E. coli survival rate under 3HP stress. This study shed light on clues for developing E. coli strains with higher resistance to 3HP toxicity and lower production cost for industrial applications.

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Section: Proteins Involved In Amino Acids Metabolismsupporting

confidence: 90%

“…7 For 3HP production, toxicity starts only at the concentration of 200 mM, which is too low for its commercial production. 8,9 E. coli has the ability to remain viable under abroad range of pH conditions between pH= 2-8. It is due to the different acid resistance (AR) systems that have been identified to counteract the acid stress.…”

Section: Introductionmentioning

confidence: 99%

Development of a 3-hydroxypropionate resistantEscherichia colistrain

et al. 2016

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“…1), can also have a significant impact on product export and therefore on intracellular pH [42]. In addition to the pH-based inhibition linked to intra-and extracellular 3-HP, a specific interference of its anionic form with the cellular metabolism was reported by Warnecke et al [43], who observed that the 3-HP toxicity in E. coli involved inhibition of the chorismate and threonine superpathways. A study on K. pneumoniae showed that when 3-HP was added to the culture medium, the rates of cell growth, glycerol consumption, and 3-HP production gradually decreased as the 3-HP concentration increased between 120 and 790 mM (e.g., about four times less 3-HP production compared to culture performed without 3-HP) [17].…”

Section: Discussionmentioning

confidence: 97%

Diversity of Lactobacillus reuteri Strains in Converting Glycerol into 3-Hydroxypropionic Acid

Burgé¹,

Saulou‐Bérion²,

Moussa³

et al. 2015

Appl Biochem Biotechnol

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The present study aims at comparing the performances of three Lactobacillus reuteri strains (DSM 20016, DSM 17938, and ATCC 53608) in producing 3-hydroxypropionic acid (3-HP) from glycerol and at exploring inhibition phenomena during this bioconversion. Differences were highlighted between the three strains in terms of 3-HP production yield, kinetics of substrate consumption, and metabolite production. With a maximal productivity in non-optimal conditions (free pH) around 2 g.L(-1).h(-1) of 3-HP and 4 g.L(-1).h(-1) of 3-hydroxypropionaldehyde (3-HPA) depending on the strain, this study confirmed the potential of L. reuteri for the biotechnological production of 3-HP. Moreover, the molar ratios of 3-HP to 1,3-propanediol (1,3-PDO) obtained for the three strains (comprised between 1.25 and 1.65) showed systematically a higher 3-HP production. From these results, the DSM 17938 strain appeared to be the most promising strain. The impact of glycerol bioconversion on the bacteria's physiological state (a decrease of around 40 % in DSM 17938 cells showing an enzymatic activity after 3 h) and survival (total loss of cultivability after 2 or 3 h depending on the strains) was revealed and discussed. The effect of each metabolite on L. reuteri DSM 17938 was further investigated, displaying a drastic inhibition caused by 3-HPA, while 3-HP induced lower impact and only at acidic pH.

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“…Recently, a number of innovative approaches have been developed that balance metabolic flux at a global level through either perturbation of global transcription machinery (13), genomic-scale mapping of fitness altering genes (14,15) or multiplex automated genome engineering (16). In addition, new strategies have been developed to balance the metabolic flux within a target pathway by tuning pathway gene expression through engineering of the promoters (13), ribosome binding sites (7) and intergenic regions (5).…”

Section: Introductionmentioning

confidence: 99%

Customized optimization of metabolic pathways by combinatorial transcriptional engineering

Yuan

et al. 2012

Nucleic Acids Research

226

195

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A major challenge in metabolic engineering and synthetic biology is to balance the flux of an engineered heterologous metabolic pathway to achieve high yield and productivity in a target organism. Here, we report a simple, efficient and programmable approach named ‘customized optimization of metabolic pathways by combinatorial transcriptional engineering (COMPACTER)’ for rapid tuning of gene expression in a heterologous pathway under distinct metabolic backgrounds. Specifically, a library of mutant pathways is created by de novo assembly of promoter mutants of varying strengths for each pathway gene in a target organism followed by high-throughput screening/selection. To demonstrate this approach, a single round of COMPACTER was used to generate both a xylose utilizing pathway with near-highest efficiency and a cellobiose utilizing pathway with highest efficiency that were ever reported in literature for both laboratory and industrial yeast strains. Interestingly, these engineered xylose and cellobiose utilizing pathways were all host-specific. Therefore, COMPACTER represents a powerful approach to tailor-make metabolic pathways for different strain backgrounds, which is difficult if not impossible to achieve by existing pathway engineering methods.

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Rapid dissection of a complex phenotype through genomic-scale mapping of fitness altering genes

Cited by 44 publications

References 39 publications

Development of a 3-hydroxypropionate resistantEscherichia colistrain

Development of a 3-hydroxypropionate resistantEscherichia colistrain

Diversity of Lactobacillus reuteri Strains in Converting Glycerol into 3-Hydroxypropionic Acid

Customized optimization of metabolic pathways by combinatorial transcriptional engineering

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