Publications by authors named "Tian-Qiong Shi"

Abscisic acid (ABA), a crucial phytohormone, is industrially synthesized using Botrytis cinerea and has wide-ranging applications in agriculture, forestry, and environmental conservation. However, the industrial fermentation of ABA using B. cinerea still faces numerous challenges.

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Terpenoids, known for their structural and functional diversity, play a significant role in various fields such as energy, cosmetics, pharmaceuticals, and fragrances. With the increasing globalization of the fragrance and flavor market, there is an urgent need to develop microbial cell factories to sustainably produce terpenoids through fermentation using renewable raw materials. With advancements in biotechnology, constructing efficient microbial cell factories for the heterologous synthesis of terpenoids to meet production demands has become feasible.

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Abscisic acid (ABA), a pivotal plant growth regulator, is extensively utilized in agricultural production, ecological vegetation restoration, and landscape greening. Although remains the primary strain for industrial ABA production, its suboptimal efficiency limits large-scale applications. Recent advancements have elucidated the biosynthetic pathway of ABA.

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A genetic algorithm-optimized neural network (ANN-GA) was developed for real-time monitoring of gibberellin (GA3) production during Fusarium fujikuroi fermentation. This model addresses the limitations of traditional off-line detection methods, such as contamination risks and delayed feedback, by integrating six critical inputs-initial glucose concentration, fermentation time, temperature, pH, dissolved oxygen, and rotational speed-to predict glucose consumption and GA3 synthesis with an accuracy of 99.41%.

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Gibberellin GA3 is a plant growth regulator with significant applications in agriculture, and has gained attention as an excellent host for the industrial production of GA3. Although numerous gene-editing tools have been developed, the precise metabolic flux regulation in was significantly hindered because the endogenous promoters were rarely identified. In this study, a library containing 20 potential promoters was mined and constructed for the first time through transcriptome sequencing.

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Filamentous fungi are essential industrial microorganisms that can serve as sources of enzymes, organic acids, terpenoids, and other bioactive compounds with significant applications in food, medicine, and agriculture. However, the underdevelopment of gene editing tools limits the full exploitation of filamentous fungi, which still present numerous untapped potential applications. In recent years, the CRISPR/Cas (clustered regularly interspaced short palindromic repeats) system, a versatile genome-editing tool, has advanced significantly and been widely applied in filamentous fungi, showcasing considerable research potential.

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Abscisic acid (ABA) is an important plant growth regulator with broad applications in agriculture, forestry, and other fields. Currently, the industrial production of ABA primarily relies on microbial fermentation using , but its genetic toolbox is limited. To address this, we first screened 10 strong constitutive promoters from the genome of through transcriptomic analysis.

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Article Synopsis
  • Genome engineering is a vital tool across scientific fields that improves human welfare and addresses challenges, with CRISPR-Cas being the most prominent method used for modifying genomes.
  • The limitations of the CRISPR-Cas system, notably its reliance on double-strand breaks and variable editing efficiency, have spurred interest in CRISPR-associated transposons (CASTs), which can integrate DNA with high precision and without depending on the host's DNA repair processes.
  • This review discusses the advancements and challenges of CASTs, highlighting their potential to revolutionize genome editing by expanding available techniques beyond conventional methods.
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The development of high-performance strains and the continuous breakthrough of strain screening technology also pose challenges to downstream fermentation optimization and scale-up. Therefore, neural network models are utilized to optimize the fermentation process to meet the goals of boosting yield or lowering cost, with the use of artificial intelligence technology in conjunction with the peculiarities of the fermentation process. High-performance strains' yield rise and fermentation process amplification will be sped up with the aid of neural network models.

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  • Adaptive laboratory evolution is a method that researchers use to improve the traits of microorganisms, and it's now being applied to non-model strains like Yarrowia lipolytica, which has industrial applications.
  • This approach addresses challenges posed by specific substances and environmental factors that can negatively impact Yarrowia lipolytica's activity.
  • The manuscript summarizes experiments focusing on enhancing lignocellulose utilization and production in Yarrowia lipolytica, and discusses how adaptive laboratory evolution can be paired with other techniques to better understand how these strains evolve.
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Article Synopsis
  • * Core to biomanufacturing are cell factories, which face challenges like low productivity and metabolic imbalances due to conflicts between natural product production and cell growth.
  • * Enzyme co-localization strategies offer a promising approach to optimize these cell factories, and the article reviews applications across various compartmentalization techniques while suggesting future research directions.
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Flavonoids, a significant group of natural polyphenolic compounds, possess a broad spectrum of pharmacological effects. Recent advances in the systematic metabolic engineering of yeast cell factories (YCFs) provide new opportunities for enhanced flavonoid production. Herein, we outline the latest research progress on typical flavonoid products in YCFs.

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Article Synopsis
  • - Monoterpenoids are key compounds found in various industries like energy, cosmetics, and pharmaceuticals, and their microbial synthesis, particularly through yeasts, is gaining interest due to benefits like fast growth and advanced genetic techniques.
  • - Recent improvements in metabolic and fermentation engineering have boosted the production of monoterpenoids by optimizing biosynthetic pathways and addressing challenges like cytotoxicity and substrate use.
  • - The review not only covers the latest strategies for enhancing monoterpenoid production and highlights specific examples, but also discusses future directions for creating efficient "cell factories" for these valuable compounds.
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5-Aminolevulinic acid (5-ALA) is a non-proteinogenic amino acid essential for synthesizing tetrapyrrole compounds, including heme, chlorophyll, cytochrome, and vitamin B12. As a plant growth regulator, 5-ALA is extensively used in agriculture to enhance crop yield and quality. The complexity and low yield of chemical synthesis methods have led to significant interest in the microbial synthesis of 5-ALA.

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Gibberellic acid (GA3) is a vital plant growth hormone widely used in agriculture. Currently, GA3 production relies on liquid fermentation by the filamentous fungus . However, the lack of an effective selection marker recycling system hampers the application of metabolic engineering technology in , as multiple-gene editing and positive-strain screening still rely on a limited number of antibiotics.

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Article Synopsis
  • Gibberellic acid (GA3) is a vital plant growth regulator produced by the fungus Fusarium fujikuroi, but a limited understanding of its metabolic pathways has challenged efforts to optimize its production.
  • This study introduced a new technology using small-molecule compounds that significantly increased GA3 production, particularly with the addition of terbinafine, which raised levels to 1.08 g/L.
  • By analyzing lipid and squalene biosynthesis pathways, researchers implemented metabolic engineering and lipid substrate supplementation, ultimately achieving a GA3 yield of 3.24 g/L in a 5 L bioreactor using waste cooking oil as the carbon source.
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  • - Metabolic engineering of yeast is essential for enhancing cell factory productivity, focusing on the stable integration of external DNA into the yeast genome.
  • - The research developed an advanced toolkit called YALIcloneHR, which utilizes modular cloning, homologous arms, and CRISPR technology to facilitate gene-specific knockout and integration in Yarrowia lipolytica.
  • - The approach was tested by knocking out the PEX10 gene, leading to a recombinant strain capable of producing 4.8% arachidonic acid, indicating potential for future chemical production from acetyl-CoA.
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Liquid fermentation is the primary method for GA production using. However, production capacity is limited due to unknown metabolic pathways. To address this, we constructed a genome-scale metabolic model (CY1235) with 1753 reactions, 1979 metabolites, and 1235 genes to understand the GA regulation mechanisms.

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Patchoulol is an important sesquiterpene alcohol with a strong and lasting odor, which has led to prominent applications in perfumes and cosmetics. In this study, systematic metabolic engineering strategies were adopted to create an efficient yeast cell factory for patchoulol overproduction. First, a baseline strain was constructed by selecting a highly active patchoulol synthase.

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  • * Recent advances in metabolic engineering have enabled the creation of microbial cell factories, particularly yeasts, for the industrial synthesis of β-carotene due to their safety and efficiency.
  • * The review details innovative strategies for enhancing β-carotene biosynthesis, such as protein and promoter engineering, and suggests future approaches for optimizing production.
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Background: α-Humulene is an important biologically active sesquiterpene, whose heterologous production in microorganisms is a promising alternative biotechnological process to plant extraction and chemical synthesis. In addition, the reduction of production expenses is also an extremely critical factor in the sustainable and industrial production of α-humulene. In order to meet the requirements of industrialization, finding renewable substitute feedstocks such as low cost or waste substrates for terpenoids production remains an area of active research.

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  • Arachidonic acid (ARA) is an important ω-6 fatty acid crucial for heart health and brain development, with significant use in food and pharmaceuticals.
  • Traditional sources of ARA, mainly deep-sea fish oil, are limited and threaten fish populations, prompting the search for alternative production methods.
  • Recent advancements in synthetic biology have made oleaginous fungi a viable and promising option for large-scale ARA production, utilizing technologies like metabolic engineering and fermentation regulation to enhance yield.
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Gibberellic acid (GA3) is a plant growth hormone that plays an important role in the production of crops, fruits, and vegetables with a wide market share. Due to intrinsic advantages, liquid fermentation of Fusarium fujikuroi has become the sole method for industrial GA3 production, but the broader application of GA3 is hindered by low titer. In this study, we combined atmospheric and room-temperature plasma (ARTP) with ketoconazole-based screening to obtain the mutant strain 3-6-1 with high yield of GA3.

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