Theoretical feasibility based biosynthetic pathway evaluation method
WEI Yixin1,2, HAN Yilei1, LU Diannan1, QIU Tong1,2
1. Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; 2. Beijing Key Laboratory of Industrial Big Data System and Application, Beijing 100084, China
Abstract：Synthetic biology employs cells and enzymes to produce high-value-added chemicals through biocatalytic processes. Synthetic biology uses renewable biomass as the substrate as well as the energy source, thus meeting the requirements of green and sustainable chemical engineering. In synthetic biology, metabolic pathway reconstruction is a key step in the development of industrial strains and the biocatalytic synthesis of chemicals, which aims to determine the reaction pathways and substrates for the synthesis of target compounds in the host; and metabolic pathway reconstruction is the basis for the directed evolution of enzymes and the biosynthesis of target substances. Considering the complexity of the biological metabolic network, a metabolic pathway reconstruction typically results in numerous pathway results. To improve efficiency and reduce invalid experimental attempts, reasonable and effective pathway evaluation and screening are highly important. Current evaluation methods of relevant pathway reconstruction tools are relatively simple, using a few indicators without prioritizing any of them. To solve this problem, this paper proposes a biosynthetic pathway evaluation method. Metabolic path reconstruction generally includes path acquisition and evaluation. The path evaluation process can score and rank the most optimal candidate paths and make recommendations based on the ranking results to obtain several candidate paths to synthesize the target product. This study achieved path acquisition based on the Rhea database. The proposed path evaluation method designed six path evaluation indicators and calculated different path characteristics of several candidate paths, which indicated the path theoretical feasibility, including the path length score, the proportion of real reactions from the database, the path molecular similarity score, the path feasibility score, the proportion of reactions with enzyme information, and the reaction rules feasibility score. These characteristics reflected the theoretical feasibility of biosynthetic pathways from different aspects. To realize the scientific-weighted summation of the indicators, their individual weights were determined using the analytic hierarchy process. Three experts were invited to give the judgment matrices based on their subjective judgments of the relative importance of the indicators. Using these matrices, the respective indicator weights were calculated. Combined with the consistency index, the indicator weights determined by different experts were fused to obtain the final composite index weight, which was subsequently used to calculate the final path score for each path. The effectiveness of the biosynthetic path evaluation method established in this study is demonstrated by an actual test of conversion between benzoate and 2, 3-dihydroxybenzoate. The evaluation score for each path is calculated and used to provide reasonable and interpretable path recommendations. Paths with higher evaluation scores offer advantages in terms of theoretical feasibility. The proposed path evaluation method achieves the expected results, which can be used to deal with the contradiction between the richness of data and difficulty of practice in synthetic biology, reduce the trial-and-error cost of experiments, and provide a basis for increasing the practicability of biological retrosynthesis tools.
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2023, Vol. 63 
