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Omics approaches have been applied to understand the boosted productivity of natural products by industrial high-producing microorganisms. Here, with the updated genome sequence and transcriptomic profiles derived from high-throughput sequencing, we exploited comparative omics analysis to further enhance the biosynthesis of erythromycin in an industrial overproducer, Saccharopolyspora erythraea HL3168 E3. By comparing the genome of E3 with the wild type NRRL23338, we identified fragment deletions inside 56 coding sequences and 255 single nucleotide polymorphisms over the genome of E3. Substantial numbers of genomic variations were observed in genes responsible for pathways which were interconnected to the biosynthesis of erythromycin by supplying precursors/cofactors or by signal transduction. Through comparative transcriptomic analysis, L-glutamine/L-glutamate and 2-oxoglutarate were identified as reporter metabolites. Around the node of 2-oxoglutarate, genomic mutations were also observed. Furthermore, the transcriptomic data suggested that genes involved in the biosynthesis of erythromycin were significantly up-regulated constantly, whereas some genes in biosynthesis clusters of other secondary metabolites contained nonsense mutations and were expressed at extremely low levels. Based on the omics association analysis, readily available strategies were proposed to engineer E3 by simultaneously overexpressing sucB (coding for 2-oxoglutarate dehydrogenase E2 component) and sucA (coding for 2-oxoglutarate dehydrogenase E1 component), which increased the erythromycin titer by 71% compared to E3 in batch culture. This work provides more promising molecular targets to engineer for enhanced production of erythromycin by the overproducer.

Formation of chlorate (ClO3−) and perchlorate (ClO4−) as by-products in electrooxidation process has raised concern. In the present study, the formation of ClO3− and ClO4− in the presence of 1.0 mM Cl− on boron doped diamond (BDD) and Magneli phase titanium suboxide (Ti4O7) anodes were evaluated. The Cl− was transformed to ClO3− (temporal maximum 276.2 µM) in the first 0.5 h on BDD anodes with a constant current density of 10 mA cm2, while approximately 1000 µM ClO4− was formed after 4.0 h. The formation of ClO3− on the Ti4O7 anode was slower, reaching a temporary maximum of approximately 350.6 µM in 4.0 h, and the formation of ClO4− was also slower on the Ti4O7 anode, taking 8.0 h to reach 780.0 µM. Compared with the BDD anode, the rate of ClO3− and ClO4− formation on the Ti4O7 anode were always slower, regardless of the supporting electrolytes used in the experiments, including Na2SO4, NaNO3, Na2B4O7, and Na2HPO4. It is interesting that the formation of ClO4− during electrooxidation was largely mitigated or even eliminated, when methanol, KI, and H2O2 were included in the reaction solutions. The mechanism of the inhibition on Cl− transformation by electrooxidation was explored.

The use of differentiating human induced pluripotent stem cells (hiPSCs) in mini-tissue organoids provides an invaluable resource for regenerative medicine applications, particularly in the field of disease modeling. However, most studies using a kidney organoid model, focused solely on the transcriptomics and did not explore mechanisms of regulating kidney organoids related to metabolic effects and maturational phenotype. Here, we applied metabolomics coupled with transcriptomics to investigate the metabolic dynamics and function during kidney organoid differentiation. Not only did we validate the dominant metabolic alteration from glycolysis to oxidative phosphorylation in the iPSC differentiation process but we also showed that glycine, serine, and threonine metabolism had a regulatory role during kidney organoid formation and lineage maturation. Notably, serine had a role in regulating S-adenosylmethionine (SAM) to facilitate kidney organoid formation by altering DNA methylation. Our data revealed that analysis of metabolic characterization broadens our ability to understand phenotype regulation. The utilization of this comparative omics approach, in studying kidney organoid formation, can aid in deciphering unique knowledge about the biological and physiological processes involved in organoid-based disease modeling or drug screening.

Background Glucoamylase is one of the most industrially applied enzymes, produced by Aspergillus species, like Aspergillus niger. Compared to the traditional ways of process optimization, the metabolic engineering strategies to improve glucoamylase production are relatively scarce. Results In the previous study combined multi-omics integrative analysis and amino acid supplementation experiment, we predicted four amino acids (alanine, glutamate, glycine and aspartate) as the limited precursors for glucoamylase production in A. niger. To further verify this, five mutants namely OE-ala, OE-glu, OE-gly, OE-asp1 and OE-asp2, derived from the parental strain A. niger CBS 513.88, were constructed respectively for the overexpression of five genes responsible for the biosynthesis of the four kinds of amino acids (An11g02620, An04g00990, An05g00410, An04g06380 and An16g05570). Real-time quantitative PCR revealed that all these genes were successfully overexpressed at the mRNA level while the five mutants exhibited different performance in glucoamylase production in shake flask cultivation. Notably, the results demonstrated that mutant OE-asp2 which was constructed for reinforcing cytosolic aspartate synthetic pathway, exhibited significantly increased glucoamylase activity by 23.5% and 60.3% compared to CBS 513.88 in the cultivation of shake flask and the 5 L fermentor, respectively. Compared to A. niger CBS 513.88, mutant OE-asp2 has a higher intracellular amino acid pool, in particular, alanine, leucine, glycine and glutamine, while the pool of glutamate was decreased. Conclusion Our study combines the target prediction from multi-omics analysis with the experimental validation and proves the possibility of increasing glucoamylase production by enhancing limited amino acid biosynthesis. In short, this systematically conducted study will surely deepen the understanding of resources allocation in cell factory and provide new strategies for the rational design of enzyme production strains.

Background In the phase of oxygen limitation during Aspergillus niger fermentation, the cell growth decreased, while the yield of glucoamylase increased continuously and significantly. Explanation on the changes of transcriptome profile during this process may improve our understanding on mechanisms of cell adaption and enzyme production in A. niger. Results The transcriptomic data from 4 time points in oxygen limitation process of a glucoamylase production A. niger strain were analyzed. Hierarchical clustering of all samples showed that the strongest transcriptional response occurred between the early and middle stage of oxygen limitation. 515 differentially expressed genes (DEGs) were identified and were clustered into 12 expression patterns. Continuously down-regulated DEGs were significantly enriched in GO terms of the ribosome, translation, and aminoacyl-tRNA biosynthesis, and continuously up-regulated DEGs were mainly involved in GO terms of fatty acid catabolism, N-acetyltransferase activity, lipase activity, and carboxylesterase activity. Pyruvate kinase and asparagine synthetase which related to the biosynthesis of the main amino acid composition of the enzyme were significantly up-regulated. Sterol-regulatory element-binding proteins (SREBP) transcription factor SrbB was one of the most up-regulated proteins, indicating its important roles in hypoxia fermentation of A. niger. Conclusion Comparative transcriptome data analysis of the fermentation revealed that the overall reduced biosynthesis of translation machine and fatty acid, acceleration of fatty acid catabolism, and increased synthesis of main amino acid compositions of glucoamylase are the key transcriptional changes during the oxygen limitation fermentation process of A. niger.

Additional file 1: Amino acid contents of biomass protein and glucoamylase.

Additional file 2: Fig. S1. Color changes of spores of A. niger. a. The parental strain CBS 513.88 b. Gene olvA defective mutant. Fig. S2. Schematic diagram of constructions of donor DNA for olvA deletion and target gene overexpression. Fig. S3. Schematic diagram of the generation of the mutants for gene overexpression by CRISPR/Cas9 assisted homologous recombination. Fig. S4. Comparison of the mutant CBS-ΔolvA and the parental strain CBS 513.88 in shake flask fermentation. Data represent the average values and standard deviations from three replicates. Fig. S5. Growth (a) and glucoamylase production (b) profiles of the two mutants OE-asp1 and OE-asp2 and the parental strain CBS 513.88 in the 5 L fermentor. The vertical line (at 40 h) shows the beginning of the oxygen-limited phase. Data represent the average values and standard deviations from three replicates. Fig. S6. a. Relative mRNA levels of gene An04g06380 in the mutant OE-asp1. b. Relative mRNA levels of gene An16g05570 in the mutant OE-asp2. Samples were taken at 36 h (exponential growth phase) and 72 h (oxygen-limited phase) from the 5 L fermentor. Data represent the average values and standard deviations from three replicates.

Aspergillus niger, as an important industrial fermentation strain, is widely applied in the production of organic acids and industrial enzymes. With the development of diverse omics technologies, the data of genome, transcriptome, proteome and metabolome of A. niger are increasing continuously, which declared the coming era of big data for the research in fermentation process of A. niger. The data analysis from single omics and the comparison of multi-omics, to the integrations of multi-omics based on the genome-scale metabolic network model largely extends the intensive and systematic understanding of the efficient production mechanism of A. niger. It also provides possibilities for the reasonable global optimization of strain performance by genetic modification and process regulation. We reviewed and summarized progress in omics research of A. niger, and proposed the development direction of omics research on this cell factory.黑曲霉作为重要的工业发酵菌株，被广泛用于多种有机酸和工业用酶的生产。随着组学技术的日益发展和成熟，黑曲霉的基因组、转录组、蛋白质组、代谢组等组学数据不断增长，宣告着黑曲霉生物过程研究大数据时代的到来。从单一组学的数据分析、多组学的比较到以基因组代谢网络模型为中心的多组学整合研究,人们对黑曲霉高效生产机制的理解不断深入和系统，这为通过遗传改造和过程调控对菌株的生产性能进行理性的全局优化提供了可能。本文回顾和总结了近年来黑曲霉的组学研究进展，并提出黑曲霉组学研究未来的发展方向。.