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Dai, Ziyu

Publications and source records attributed to Dai, Ziyu.

At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Itaconic acid production is regulated by LaeA in Aspergillus pseudoterreus

The global regulator LaeA controls secondary metabolism in diverse Aspergillus species. Here we explored its role in regulation of itaconic acid production in Aspergillus pseudoterreus. To understand its role in regulating metabolism, we deleted and overexpressed laeA, and assessed the transcriptome, proteome, and secreted metabolome prior to and during initiation of phosphate limitation induced itaconic acid production. We found that secondary metabolite clusters, including the itaconic acid biosynthetic gene cluster, are regulated by laeA and that laeA is required for high yield production of itaconic acid. Overexpression of laeA improves itaconic acid yield at the expense of biomass by increasing the expression of key biosynthetic pathway enzymes and attenuating the expression of genes involved in phosphate acquisition and scavenging. Increased yield was observed in optimized conditions as well as conditions containing excess nutrients that may be present in inexpensive sugar containing feedstocks such as excess phosphate or complex nutrient sources. This suggests that global regulators of metabolism may be useful targets for engineering metabolic flux that is robust to environmental heterogeneity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Bayesian Inference for Integrating Yarrowia lipolytica Multiomics Datasets with Metabolic Modeling

Optimizing the metabolism of microbial cell factories for yields and titers is a critical step for economically viable production of bioproducts and biofuels. In this process, tuning the expression of individual enzymes to obtain the desired pathway flux is a challenging step, in which data from separate multiomics techniques must be integrated with existing biological knowledge to determine where changes should be made. Following a design-build-test-learn strategy, building on recent advances in Bayesian metabolic control analysis, we identify in this work key enzymes in the oleaginous yeast Yarrowia lipolytica that correlate with the production of itaconate by integrating a metabolic model with multiomics measurements. To this extent, we quantify the uncertainty for a variety of key parameters, known as flux control coefficients (FCCs), needed to improve the bioproduction of target metabolites and statistically obtain key correlations between the measured enzymes and boundary flux. Based on the top five significant FCCs and five correlated enzymes, our results show phosphoglycerate mutase, acetyl-CoA synthetase (ACSm), carbonic anhydrase (HCO3E), pyrophosphatase (PPAm), and homoserine dehydrogenase (HSDxi) enzymes in rate-limiting reactions that can lead to increased itaconic acid production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Optimizing Oil Production in Oleaginous Yeast by Cell-Wide Measurements and Genome-Based Models (Final Report)

The work funded under this DOE genomics grant focused on characterizing, modifying and developing genetic engineering tools for the then very promising but under-characterized oleaginous yeast Yarrowia lipolytica. To-date, all biodiesel production facilities rely on vegetable oils and animal fats as feedstocks, which are very limited. Nature, on the other hand, is very well equipped for making carbohydrates, which are very plentiful throughout the world and rather well distributed in various forms. While numerous (biochemical and thermochemical) technologies exist presently for carbohydrate conversion to alcohols, there is none available for the cost-efficient production of lipids from carbohydrate feedstocks. Such a technology would have wide-ranging implications in land use, renewable resource utilization and production of transportation fuels with minimal carbon footprint. The global research objectives of this award were to develop tools for cell-wide measurement of metabolites and lipids that, along with transcriptional data, will allow the construction of genome-scale metabolic models, as well as models of transcriptional regulation, that will guide the further metabolic engineering of Yarrowia lipolytica. To achieve these goals, a very strong international and diverse team consisting of research groups at MIT, UCLA, PNNL and Chalmers University was put together, whose specific goals, achievements and breakthroughs are included in this report.

10 SYNTHETIC FUELS↗
DOE OSTI2021

Genetically engineered oleaginous yeast Lipomyces starkeyi for sesquiterpene a-zingiberene production

In this study we demonstrate that transgenic Lipomyces starkeyi strains expressing a ?-zingiberene synthase gene from Lemon basil or Hall’s panicgrass can produce up to 17 mg/l of ?-zingiberene in yeast extract peptone dextrose (YPD) medium containing 4% glucose. Following these findings, the transgenic strain was examined in 8% glucose media with C/N ratios of 20 or 80, and YPD. YPD medium resulted in 59.2 mg/l??-zingiberene accumulation. We further improved ?-zingiberene production by over-expression of selected genes from mevalonate pathway and achieved 145% improvement in ?-zingiberene synthesis. The growth medium was optimized for ?-zingiberene production, which resulted in 14.9% higher titer than YPD medium. The final transgenic strain produced 700 mg/l ?-zingiberene in fed-batch bioreactor culture. This study opens a new synthetic route to produce ?-zingiberene or other terpenoids in the oleaginous yeast L. starkeyi and establishes this yeast as a platform for jet fuel biosynthesis.

Dai, Ziyu↗
DOE OSTI2021

Integration of proteomics and metabolomics into the Design, Build, Test, Learn cycle to improve 3-hydroxypropionic acid production in Aspergillus pseudoterreus

Biological engineering of microorganisms to produce value-added chemicals is a promising route to sustainable manufacturing. However, overproduction of metabolic intermediates at high titer, rate, and yield from inexpensive substrates is challenging in non-model systems where limited information is available regarding metabolic flux and its control in production conditions. Integrated multi-omic analyses of engineered strains offers an in-depth look at metabolites and proteins directly involved in growth and production of target and non-target bioproducts. Here we applied multi-omic analyses to overproduction of the polymer precursor 3-hydroxypropionic acid (3HP) in the filamentous fungus Aspergillus pseudoterreus. A synthetic pathway consisting of aspartate decarboxylase, beta-alanine pyruvate transaminase, and 3HP dehydrogenase was designed and built for A. pseudoterreus. Strains with single- and multi-copy integration events were isolated and multi-omics analysis consisting of intracellular and extracellular metabolomics and targeted and global proteomics was used to interrogate the strains in shake-flask and bioreactor conditions. Production of a variety of co-products (organic acids and glycerol) and oxidative degradation of 3HP were identified as metabolic pathways competing with 3HP production. Intracellular accumulation of nitrogen as 2,4-diaminobutanoate was identified as an off-target nitrogen sink that may also limit flux through the engineered 3HP pathway. Elimination of the high-expression oxidative 3HP degradation pathway by deletion of a putative malonate semialdehyde dehydrogenase improved the yield of 3HP by 3.4× after 10 days in shake-flask culture. This is the first report of 3HP production in a filamentous fungus amenable to industrial scale biomanufacturing of organic acids at high titer and low pH.

Pomraning, Kyle R.↗