Reconstruction And Analysis Of Genome-scale Metabolic Models Of Typical Industrial Microorganisms

To obtain more efficient use of microbial cells in biotechnology industry, it is necessaryto comprehensively understand their complex metabolism controlled by genome. Genomescale metabolic model (GSMM) sets up the relationship between genome and the complexmetabolic process. It thus offers us an efficient way to understand the target organisms.However, the heavy and complicated reconstruction limited its application in illustrating thebiological properties. In this study, an automatic reconstruction process for draft metabolicmodel was developed using MATLAB coding. The automatic process was applied to buildingthe GSMM of two typical industrial microorganisms Lactobaicllus casei and Aspergillusterreus. Based on these models, the major metabolic physiologies of the two organisms wereinvestigated. The main results included:(1) Based on protein homologous alignment, the automatic draft reconstruction processwas developed in MATLAB. The process consisted of several processing nodes, i.e. formattransformation of reference GSMM, construction of homologous relationship between targetgenes and reference GSMM, extraction of metabolic data from reference GSMM,construction of GPR association for target organism, and storing the target draft metabolicmodel in EXCEL worksheet.(2) Aided by the automatic program and L. plantarum WCFS1GSMM, the draft modelof L. casei LC2W was built, with410genes and374reactions. After refining, the functionalGSMM iJL760comprised a total of760genes,688reactions, and591metabolites. The ORFcoverage of iJL760(24.0%) is currently the highest among the available LAB GSMMs. Andmetabolic functions of247genes were re-annotated. Indicated by FBA, LC2W wasauxotrophic in synthesis ten amino acids and seven vitamins. With all these essential nutrientssupplemented, it could utilize more than twenty kinds of carbohydrates, and the supply ofoxygen could enhance its growth on carbohydrates such as ethanol. The growth was alsoindependent to75to111genes, depending on medium conditions. In glucose-limited acidsfermentation, cells tend to consume aspartate and serine. The addition of six amino acidscould enhance EPS production.(3) Aided by the automatic program, A. niger and A. oryzae GSMMs, the draft model ofA. terreus with1169reactions and1263genes was built. After curation, the final GSMMiJL1454contained1454genes,1451reactions, and1155metabolites. The ORF coverage ofiJL1454is14%, which is also currently the highest among Aspergillus GSMMs. iJL1454wascapable in predicting the growth phenotype of A. terreus on different carbon and nitrogensources, and after deletion of essential genes. The biosynthetic pathway of itaconate fromglucose included29reactions and55genes. Enzymes or proteins such as glucose kinase anditaconate transporters took key places in the production. Moreover, itaconate production andcell growth need different medium conditions, especially on pH and phosphate concentration.