Engineering of global transcription factor FruR to redirect the carbon flow in Escherichia coli for enhancing L-phenylalanine biosynthesis.

BACKGROUND: The catabolite repressor/activator protein (FruR) is a global regulatory protein known to control the expression of several genes concerned with carbon utilization and energy metabolism. This study aimed to illustrate effects of the FruR mutant on the L-phenylalanine (L-PHE) producing strain PHE01. RESULTS: Random mutagenesis libraries of fruR generated in vitro were first integrated into the chromosome of PHE01 by CRISPR/Cas9 technique, and then the best mutant PHE07 (FruRE173K) was obtained. With this mutant, a final L-PHE concentration of 70.50 ± 1.02 g/L was achieved, which was 23.34% higher than that of PHE01. To better understand the mechanism, both transcriptomes and metabolomes of PHE07 were carried out and compared to that of PHE01. Specifically, the transcript levels of genes involved in gluconeogenesis pathway, pentose phosphate pathway, Krebs cycle, and glyoxylate shunt were up-regulated in the FruRE173K mutant, whereas genes aceEF, acnB, and icd were down-regulated. From the metabolite level, the FruRE173K mutation led to an accumulation of pentose phosphate pathway and Krebs cycle products, whereas the products of pyruvate metabolism pathway: acetyl-CoA and cis-aconic acid, were down-regulated. As a result of the altered metabolic flows, the utilization of carbon sources was improved and the supply of precursors (phosphoenolpyruvate and erythrose 4-phosphate) for L-PHE biosynthesis was increased, which together led to the enhanced production of L-PHE. CONCLUSION: A novel strategy for L-PHE overproduction by modification of the global transcription factor FruR in E. coli was reported. Especially, these findings expand the scope of pathways affected by the fruR regulon and illustrate its importance as a global regulator in L-PHE production.

Pancancer survival prediction using a deep learning architecture with multimodal representation and integration.

Motivation: Use of multi-omics data carrying comprehensive signals about the disease is strongly desirable for understanding and predicting disease progression, cancer particularly as a serious disease with a high mortality rate. However, recent methods currently fail to effectively utilize the multi-omics data for cancer survival prediction and thus significantly limiting the accuracy of survival prediction using omics data. Results: In this work, we constructed a deep learning model with multimodal representation and integration to predict the survival of patients using multi-omics data. We first developed an unsupervised learning part to extract high-level feature representations from omics data of different modalities. Then, we used an attention-based method to integrate feature representations, produced by the unsupervised learning part, into a single compact vector and finally we fed the vector into fully connected layers for survival prediction. We used multimodal data to train the model and predict pancancer survival, and the results show that using multimodal data can lead to higher prediction accuracy compared to using single modal data. Furthermore, we used the concordance index and the 5-fold cross-validation method for comparing our proposed method with current state-of-the-art methods and our results show that our model achieves better performance on the majority of cancer types in our testing datasets. Availability and implementation: https://github.com/ZhangqiJiang07/MultimodalSurvivalPrediction. Supplementary information: Supplementary data are available at Bioinformatics online.

Enhanced production of ß-carotene by recombinant industrial wine yeast using grape juice as substrate.

In this study, both recombinant Saccharomyces cerevisiae T73-63 and FY-09 derived from the industrial wine yeast T73-4 and laboratory yeast FY1679-01B, respectively, were constructed and compared for their ß-carotene production in real grape juice. The results showed that highest ß-carotene content (5.89 mg/g) was found in strain T73-63, which was 2.1 fold higher than that of strain FY-09. Although the cell growth was inhibited by the metabolic burden induced by the production of heterogeneous ß-carotene, the pigment yield in T73-63 was still 1.7 fold higher than that of FY-09. Furthermore, high contents of ergosterol and fatty acid were also observed in T73-63. These results suggest that industrial wine yeast has highly active metabolic flux in mevalonate pathway, which leads to more carbon flux into carotenoid branch compared to that of laboratory yeast. The results of this study collectively suggest that in the application of recombinant strains to produce carotenoid using agro-industrial by-products as substrate, the suitable host strains should have active mevalonate pathway. For this purpose, the industrial wine yeast is a suitable candidate.

Potential of phenolic compounds in Ligustrum robustum (Rxob.) Blume as antioxidant and lipase inhibitors: Multi-spectroscopic methods and molecular docking.

Ligustrum robustum (Rxob.) Blume is traditionally served as a functional tea in China. In this work, the antioxidant activities of L. robustum (Rxob.) Blume extract (LRE) were evaluated and its inhibitory effect and mechanism on pancreatic lipase were further investigated. With the high contents of phenols (139.70 ± 1.41 mg gallic acid equivalent/g extract) and flavonoids (326.46 ± 7.36 mg rutin equivalent/g extract), LRE showed significant antioxidant activities (p < 0.05) for scavenging free radicals and hydrogen peroxide, inhibiting lipid peroxidation and providing strong reducing power. Meanwhile, LRE displayed remarkable inhibitory activity on pancreatic lipase with a low half-effective inhibitory concentration (IC50 ) of 2.469 ± 0.005 mg/ml which was further determined as non-competitive inhibition. The spectroscopic results showed that LRE inhibited the activity of pancreatic lipase by modifying the tertiary and secondary structures of lipase. Moreover, four phenolic compounds (acteoside, lipedoside A, oleuropein and ligurobustoside C) were identified from LRE by the high performance liquid chromatography-quadrupole- time of flight-mass spectrometry. In addition, according to molecular docking analysis, the four phenols could interact with pancreatic lipase by hydrogen bonds, so as to change the spatial structure of pancreatic lipase and inhibit its catalytic activity. The present results suggest that LRE not only exhibits strong antioxidant capacity but possesses effectively inhibitory activity on pancreatic lipase, which might have the potential to be developed as functional food and nutraceuticals for the prevention of metabolic diseases. PRACTICAL APPLICATION: Ligustrum robustum (Rxob.) Blume extract has been confirmed to possess antioxidant activity and lipase inhibitory activity, which indicates that the L. robustum extract has the potential to prevent oxidative stress and regulate fat metabolism. This work suggests that L. robustum extract can be served as a novel resource to prepare nutraceuticals and functional food in food industries.

Important role of catalase in the production of ß-carotene by recombinant Saccharomyces cerevisiae under H2O2 stress.

The effect of H(2)O(2) supplement on cell growth and ß-carotene productions in recombinant Saccharomyces cerevisiae CFW-01 and CFW-01 ctt1 deficiency in cytosolic catalase were investigated in shaking flasks. The results showed that supplement of H(2)O(2) (0.5 and 1.0 mM) can significantly stimulate the ß-carotene production. However, ß-carotene levels of CFW-01 ctt1Δ under 0.5 and 1 mM H(2)O(2) were 16.7 and 36.7% lower than those of CFW-01, respectively. Although lacking cytosolic catalase, no significant differences in cell growth were observed between CFW-01 ctt1Δ and CFW-01 under the same level of H(2)O(2) stress. These results suggest that ß-carotene can act as an antioxidant to protect the recombinant yeast from H(2)O(2) oxidative damage in the absence of cytosolic catalase. However, catalase still plays an important role in the production of ß-carotene under H(2)O(2) stress. If catalase can not timely decompose H(2)O(2), the free radicals such as OH· derived from H(2)O(2) can result in decrease of ß-carotene concentration. Therefore, in the production of ß-carotene by H(2)O(2) stress, not only the level of oxidative stress, but also the activities of catalase in cells should be considered.