Stoichiometry and kinetics of single and mixed substrate uptake in Aspergillus niger

A nutrition algorithm to optimize feed and medium composition using genome-scale metabolic models

The optimization of animal feeds and cell culture media are problems of interest to a wide range of industries and scientific disciplines. Both problems are dictated by the properties of an organism's metabolism. However, due to the tremendous complexity of metabolic systems, it can be difficult to predict how metabolism will respond to changes in nutrient availability. A common tool used to capture the complexity of metabolism in a computational framework is a genome-scale metabolic model (GEM). GEMs are useful for predicting the fluxes of reactions within an organism's metabolism. To optimize feed or media, in silico experiments can be performed with GEMs by systematically varying nutritional constraints and predicting metabolic activity. In this way, the influence of various nutritional changes on metabolic outcomes can be evaluated. However, this methodology does not guarantee an optimal solution. Here, we develop a nutrition algorithm that utilizes linear programming to search the entire flux solution space of possible dietary intervention strategies to identify the most efficient changes to nutrition for a desirable metabolic outcome. We illustrate the utility of the nutrition algorithm on GEMs of Atlantic salmon (Salmo salar) and Chinese hamster ovary (CHO) cell metabolism and find that the nutrition algorithm makes predictions that not only align with experimental findings but reveal new insights into promising feeding strategies. We show that the nutrition algorithm is highly versatile and customizable to meet the user's needs. For instance, we demonstrate that the nutrition algorithm can be used to predict feed/media compositions that maximize profit margins. While the nutrition algorithm can be used to define an optimal feed/medium ab initio, it can also identify minimal changes to be made to an existing feed/medium to drive the largest metabolic shift. Moreover, the nutrition algorithm can target multiple metabolic pathways simultaneously with only a marginal increase in computational expense. While the nutrition algorithm has its limitations, we believe that this tool can be leveraged in a broad range of biotechnological applications to enhance the feed/medium optimization process.

Microbiota drive insoluble polysaccharides utilization via microbiome-metabolome interplay during Pu-erh tea fermentation

Polysaccharides are abundant components in Pu-erh tea, yet the utilization of insoluble polysaccharides under the actions of microbiota has rarely been studied. The aim of this work was to study how insoluble polysaccharides were utilized during fermentation through the investigation of the variations and correlation of microbiota with polysaccharides degradation products. Genomics study revealed the significant changes of microbiota. Metabolomics analysis showed monosaccharides (types 1 and 3) were consumed during early and middle fermentation stages, while carboxylic acids and other monosaccharides (type 2) were accumulated at middle and late pile-fermentation stages. Correlation revealed that type 1 and 3 monosaccharides, which act as energy providers, were positively associated with Aspergillus, while type 2 monosaccharides possessing multiple bioactivities and carboxylic acids influencing tea taste were positively related to Rasamsonia, Thermomyces, Bacillaceae, and Lactobacillaceae. This study would be beneficial to improve production efficiency and provide basis for quality control of Pu-erh tea fermentation.

Engineering marine fungi for conversion of D-galacturonic acid to mucic acid

BACKGROUND

Two marine fungi, a Trichoderma sp. and a Coniochaeta sp., which can grow on D-galacturonic acid and pectin, were selected as hosts to engineer for mucic acid production, assessing the suitability of marine fungi for production of platform chemicals. The pathway for biotechnologcial production of mucic (galactaric) acid from D-galacturonic acid is simple and requires minimal modification of the genome, optimally one deletion and one insertion. D-Galacturonic acid, the main component of pectin, is a potential substrate for bioconversion, since pectin-rich waste is abundant.

RESULTS

Trichoderma sp. LF328 and Coniochaeta sp. MF729 were engineered using CRISPR-Cas9 to oxidize D-galacturonic acid to mucic acid, disrupting the endogenous pathway for D-galacturonic acid catabolism when inserting a gene encoding bacterial uronate dehydrogenase. The uronate dehydrogenase was expressed under control of a synthetic expression system, which fucntioned in both marine strains. The marine Trichoderma transformants produced 25 g L-1 mucic acid from D-galacturonic acid in equimolar amounts: the yield was 1.0 to 1.1 g mucic acid [g D-galacturonic acid utilized]-1. D-Xylose and lactose were the preferred co-substrates. The engineered marine Trichoderma sp. was more productive than the best Trichoderma reesei strain (D-161646) described in the literature to date, that had been engineered to produce mucic acid. With marine Coniochaeta transformants, D-glucose was the preferred co-substrate, but the highest yield was 0.82 g g-1: a portion of D-galacturonic acid was still metabolized. Coniochaeta sp. transformants produced adequate pectinases to produce mucic acid from pectin, but Trichoderma sp. transformants did not.

CONCLUSIONS

Both marine species were successfully engineered using CRISPR-Cas9 and the synthetic expression system was functional in both species. Although Coniochaeta sp. transformants produced mucic acid directly from pectin, the metabolism of D-galacturonic acid was not completely disrupted and mucic acid amounts were low. The D-galacturonic pathway was completely disrupted in the transformants of the marine Trichoderma sp., which produced more mucic acid than a previously constructed T. reesei mucic acid producing strain, when grown under similar conditions. This demonstrated that marine fungi may be useful as production organisms, not only for native enzymes or bioactive compounds, but also for other compounds.

The fungus Aspergillus niger consumes sugars in a sequential manner that is not mediated by the carbon catabolite repressor CreA

In nature, the fungus Aspergillus niger degrades plant biomass polysaccharides to monomeric sugars, transports them into its cells, and uses catabolic pathways to convert them into biochemical building blocks and energy. We show that when grown in liquid cultures, A. niger takes up plant-biomass derived sugars in a largely sequential manner. Interestingly, this sequential uptake was not mediated by the fungal general carbon catabolite repressor protein CreA. Furthermore, transcriptome analysis strongly indicated that the preferential use of the monomeric sugars is arranged at the level of transport, but it is not reflected in transcriptional regulation of sugar catabolism. Therefore, the results indicate that the regulation of sugar transport and catabolism are separate processes in A. niger.