Quantitative metabolic flux analysis revealed uneconomical utilization of ATP and NADPH in Acremonium chrysogenum fed with soybean oil

Optimization and Scale-Up of Fermentation Processes Driven by Models

In the era of sustainable development, the use of cell factories to produce various compounds by fermentation has attracted extensive attention; however, industrial fermentation requires not only efficient production strains, but also suitable extracellular conditions and medium components, as well as scaling-up. In this regard, the use of biological models has received much attention, and this review will provide guidance for the rapid selection of biological models. This paper first introduces two mechanistic modeling methods, kinetic modeling and constraint-based modeling (CBM), and generalizes their applications in practice. Next, we review data-driven modeling based on machine learning (ML), and highlight the application scope of different learning algorithms. The combined use of ML and CBM for constructing hybrid models is further discussed. At the end, we also discuss the recent strategies for predicting bioreactor scale-up and culture behavior through a combination of biological models and computational fluid dynamics (CFD) models.

Metabolomics profiling reveals the mechanism of increased pneumocandin B0 production by comparing mutant and parent strains

Metabolic profiling was used to discover mechanisms of increased pneumocandin B₀ production in a high-yield strain by comparing it with its parent strain. Initially, 79 intracellular metabolites were identified, and the levels of 15 metabolites involved in six pathways were found to be directly correlated with pneumocandin B₀ biosynthesis. Then by combining the analysis of key enzymes, acetyl-CoA and NADPH were identified as the main factors limiting pneumocandin B₀ biosynthesis. Other metabolites, such as pyruvate, α-ketoglutaric acid, lactate, unsaturated fatty acids and previously unreported metabolite γ-aminobutyric acid were shown to play important roles in pneumocandin B₀ biosynthesis and cell growth. Finally, the overall metabolic mechanism hypothesis was formulated and a rational feeding strategy was implemented that increased the pneumocandin B₀ yield from 1821 to 2768 mg/L. These results provide practical and theoretical guidance for strain selection, medium optimization, and genetic engineering for pneumocandin B₀ production.

Comparative expression profiling of genes involved in primary metabolism in high-yield and wild-type strains of Acremonium chrysogenum

Cephalosporin C (CPC) productivity of Acremonium chrysogenum has been improved significantly through classical strain improvement programs. Here, we used transcription and metabolite profiling to address mechanisms underlying CPC production in a high yield (HY) strain. Transcription and metabolite profiling indicated that enzymes involved in amino acid production are higher in abundance in the HY strain. Moreover, results indicate a higher flow of precursors from the glycolysis and gluconeogenesis pathways to serine synthesis at the late stage of fermentation in the HY strain. In addition, less pyruvate would enter the TCA cycle thus favoring valine synthesis. Amino acid production would also benefit from a more active pentose phosphate pathway and γ-amino butyric acid shunt both generating NADPH. Moreover the glyoxylate pathway seems to be more active in the HY strain. These results may provide new leads for CPC strain improvement in industry.

Controlling the feed rate of glucose and propanol for the enhancement of erythromycin production and exploration of propanol metabolism fate by quantitative metabolic flux analysis

In this paper, several different fermentation experiments were designed to address whether modulating glucose and propanol feeds could benefit the production level of erythromycin during pilot plant (30 L) fermentation. Results showed that glucose feed rate (determined by a set high or low culture pH) had no effect on erythromycin production, indicating that glucose was not the limiting factor for erythromycin biosynthesis under these conditions. It was found that decreasing glucose feed could stimulate the consumption of propanol, and the high erythromycin production (12.49 ± 0.50 mg ml⁻¹) was achieved by controlling the feed rates of glucose and propanol. The quantitative metabolic flux analysis disclosed that high propanol consumption increased the pool size of propionyl-CoA (~2.147 mmol g⁻¹ day⁻¹) and methylmalonyl-CoA (~1.708 mmol g⁻¹ day⁻¹). It was also found that 45-77 % of the propanol went into the TCA cycle which strengthened the conclusion that blocking the propionate pathway to TCA cycle could lead to a significant increase in erythromycin production in carbohydrate-based media (Reeves et al. Ind Microbiol Biotechnol 7:600-609, 2006). In addition, the results also suggested that a relative low intracellular ATP level resulting from low glucose feed did not limit the erythromycin biosynthesis, and a relatively high NADPH should be beneficial for erythromycin biosynthesis.