No abstract

No abstract

SignificanceTechnological advances enable increasingly comprehensive profiling of the molecular landscapes of cells, and these data can inform the personalized treatment of complex diseases. Two major obstacles are the complexity of these data and the high degree of person-to-person heterogeneity. We develop a highly simplified, personalized data representation by comparing the profile of an individual to the range of landscapes in a baseline population, thereby mimicking basic clinical diagnostic testing for departures of selected variables from normal levels. Moreover, our method can be applied to any data modality and at any level of granularity, from single features to any subset of features treated as a single entity, for example the gene expression levels in a pathway. Experiments involve both healthy human tissues and various cancer subtypes.

BackgroundL-phenylalanine (L-Phe) is an essential amino acid for mammals and applications expand into human health and nutritional products. In this study, a system level engineering was conducted to enhance L-Phe biosynthesis in Escherichia coli.ResultsWe inactivated the PTS system and recruited glucose uptake via combinatorial modulation of galP and glk to increase PEP supply in the Xllp01 strain. In addition, the HTH domain of the transcription factor TyrR was engineered to decrease the repression on the transcriptional levels of L-Phe pathway enzymes. Finally, proteomics analysis demonstrated the third step of the SHIK pathway (catalyzed via AroD) as the rate-limiting step for L-Phe production. After optimization of the aroD promoter strength, the titer of L-Phe increased by 13.3%. Analysis of the transcriptional level of genes involved in the central metabolic pathways and L-Phe biosynthesis via RT-PCR showed that the recombinant L-Phe producer exhibited a great capability in the glucose utilization and precursor (PEP and E4P) generation. Via systems level engineering, the L-Phe titer of Xllp21 strain reached 72.9 g/L in a 5 L fermenter under the non-optimized fermentation conditions, which was 1.62-times that of the original strain Xllp01.ConclusionThe metabolic engineering strategy reported here can be broadly employed for developing genetically defined organisms for the efficient production of other aromatic amino acids and derived compounds.Electronic supplementary materialThe online version of this article (10.1186/s12896-018-0418-1) contains supplementary material, which is available to authorized users.