METABOLIC ENGINEERING代谢工程
METABOLIC ENGINEERING(英文缩写 METAB ENG),ISSN 1096-7176,eISSN 1096-7184,中文译名:代谢工程 是一本学术期刊。本页汇总该期刊的最新影响因子、分区信息以及最新收录于 PubMed 的文献,帮助您快速了解期刊全貌。
发文量统计区间：2025-09-27 至 2026-09-27，按本站收录文献的发表日期统计。
期刊介绍
历年影响因子趋势
| JCR 数据年份 | 影响因子 | JCR 分区 |
|---|---|---|
| 2021 | 8.829 | Q1 |
| 2022 | 8.400 | Q1 |
| 2023 | 6.800 | Q1 |
| 2024 | 6.800 | Q1 |
| 2025 | 7.300 | Q1 |
METABOLIC ENGINEERING 最新收录文献
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1. Flux rewiring enables native D-glucosamine production in Escherichia coli.
PMID:日期:2026-11-01D-Glucosamine is an industrially important amino sugar used in pharmaceuticals, nutraceuticals, and functional materials, yet its production remains dominated by chemical extraction from chitinous biomass, raising sustainability and allergen concerns. Escherichia coli natively synthesizes D-glucosamine directly from D-glucose through endogenous metabolism, revealing an underutilized amino sugar biosynthetic capability. Building on this native pathway, D-glucosamine production was enhanced through targeted genetic modifications and systematic optimization of nitrogen metabolism and cultivation conditions, reaching 9.2 g L under shake-flask conditions. This work extends a phosphorylation-dephosphorylation strategy previously developed for neutral rare sugars to amino sugar biosynthesis, demonstrating the broader applicability of this metabolic design principle. Phosphatase identity emerged as a key control point for product formation: YbiV was the most effective phosphatase for selective D-glucosamine production, whereas alternative phosphatases redirected flux toward D-sedoheptulose. This enzyme-dependent flux partitioning further enabled tunable co-production of D-glucosamine and D-sedoheptulose. Native amino sugar biosynthesis in E. coli provides a controllable framework for producing chemically distinct sugars through endogenous metabolism and establishes a generalizable strategy for engineering amino sugar and other nitrogen-containing metabolite biosynthesis.
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2. Global transcriptional rewiring and dual-compartment engineering for efficient 3-hydroxypropionic acid production in Saccharomyces cerevisiae.
PMID:日期:2026-11-013-Hydroxypropionic acid is an important malonyl-CoA-derived platform chemical whose efficient biosynthesis is constrained by limited utilization of malonyl-CoA across subcellular compartments. Using a biosensor-guided transcription factor mutagenesis screen combined with transcriptomic and functional validation, we identify four positive mutants NRG1_R224H, STB3_L52Y, PDR1_T820C and PGD1_V243D that increase cytosolic malonyl-CoA accumulation by globally reprogramming transcription to reinforce central carbon flux and acetyl-CoA precursor supply, and remodel amino acid, redox, and lipid metabolism to favor malonyl-CoA accumulation. We further utilize mitochondrial malonyl-CoA for 3-HP production through dynamic control of HFA1 and optimized POS5 expression, and further develop a dual-compartment coordination strategy to efficiently exploit cytosolic and mitochondrial malonyl-CoA pools. Integration of optimized pathways in diploid strains enables coordinated precursor utilization, achieving 81.8 g/L 3-HP in 5-L fed-batch fermentation, the highest titer reported to date in Saccharomyces cerevisiae. This work establishes a generalizable framework for multi-compartment malonyl-CoA utilization in eukaryotic cell factories.
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3. A dual-dimensional CRISPR toolkit enables one-step high-efficiency multiplex genome editing in Komagataella phaffii.
PMID:日期:2026-11-01Against the backdrop of green biomanufacturing, engineering methanol-utilizing Komagataella phaffii (K. phaffii) represents an effective strategy to expand the one carbon (C1) product profile and speed up the industrialization of C1-based bioeconomy. To address the technical challenges of low efficiency and cumbersome experimental procedures for multiplex gene editing and precise large-fragment integration during the reconstruction of complex metabolic pathways in K. phaffii, this study established a CRISPR toolkit - Efficient Multi-Gene Editing System 3.0 (EMGES 3.0) - which enabled one-step large-fragment integration coupled with multiplex gene knockout. EMGES 3.0 was constructed through the synergistic optimization of a repair-engineered chassis and an episomal CRISPR vector. For chassis engineering, five DNA repair modules: Δlig4 (DNA Ligase IV, non-homologous end joining end ligation), ppMRE11(The endogenous MRE11 gene from Pichia pastoris) overexpression (The Meiotic Recombination 11, DNA double-strand break end resection), Δrad9 (Radiation-Sensitive 9, DNA damage checkpoint regulation), Δmph1 (Mutator Phenotype Helicase 1, improvement of homologous recombinant strand extension), and PapRecT-PaSSB co-expression (stabilization of recombination intermediates) were integrated to generate the highly recombinogenic strain Y09. For vector engineering, cenARS was replaced by panARS and the endogenous promoter P was employed to drive the double hammerhead ribozyme-single guide RNA-hepatitis delta virus ribozyme (double HH-sgRNA-HDV: dHgH)-mediated sgRNA expression, yielding the optimized vector Nov_pGAP_panARS_pLAT1_Cas9. These two features on K. phaffii together enhanced the EMGES 3.0 to a higher standard of transformation rate and editing efficiency. According to our results, EMGES 3.0 achieved dual-functional gene knockout efficiencies between 76.6% and 100%. For insertion of medium-long fragments (>4.5 kb), the efficiency achieved 93.3%. In addition, the one-step integration of ultra-long fragments (>16 kb) achieved 14.8%, which was reported for the first time. Furthermore, the efficiency of simultaneous long-fragment integration at three neutral loci reached 38.4% (>15 kb). We applied the system for one-step production of free fatty acids (FFAs, yield: 5.82 ∼ 7.30 mg/L/OD) and resveratrol (yield: 1.14 ∼ 1.28 mg/L) using methanol as the sole carbon source. EMGES 3.0 provides a robust technical foundation for complex compounds biosynthesis and high-yield industrial strains, while also advancing K. phaffii as an industrial synthetic biology chassis for efficient C1 utilization.
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4. Inducible flocculation in Komagataella phaffii enables enhanced biomass separation for biopharmaceutical production.
PMID:日期:2026-11-01Biomass separation represents a critical bottleneck in Komagataella phaffii-based biopharmaceutical processes, as typically high cell densities of 40 - 50 % create significant operational, technical and economic challenges for harvest operations. Yeast cell aggregation (flocculation) provides a solution to accelerate cell sedimentation by increasing particle size, thus allowing to improve biomass-supernatant separation efficiency during both natural gravity settling and (continuous) centrifugation operations. This study demonstrates successful engineering of K. phaffii strains with an inducible flocculation phenotype using CRISPR/Cas9-based genome editing to integrate the Saccharomyces cerevisiae FLO1 (ScFLO1) gene under control of various regulatory elements, including methanol-inducible and derepressible promoters. Flocculation strength could be enhanced by implementing transcriptional positive feedback circuits based on the methanol-inducible AOX1 promoter. To address methanol-free production requirements, we developed alternative systems to retrofit P-based ScFLO1 expression and exploited the derepressible PDF promoter, offering broader compatibility with biopharmaceutical manufacturing facilities. Flocculating cells cultivated in a bioreactor demonstrated significantly improved sedimentation behavior, with considerably lower supernatant turbidity after short low-speed centrifugation or gravity sedimentation compared to non-flocculating controls. Crucially, cell flocculation had no negative impact on product amount and quality when expressing a multivalent NANOBODY® VHH molecule with pharmaceutical relevance. Thus, this work establishes the first genetically engineered flocculation system in K. phaffii compatible with recombinant protein production, providing the basis for an innovative approach to streamline harvest operations in biopharmaceutical processes.
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5. Metabolic engineering of Candida yeasts for biotechnological applications.
PMID:日期:2026-11-01Candida yeasts represent a versatile yet underexploited platform for industrial biotechnology. These yeasts utilize a remarkably broad range of carbon sources, particularly for hydrophobic carbon sources, coupled with robust growth and diverse biosynthetic capacities, making them promising hosts for sustainable production of chemicals, fuels, and proteins. Despite these advantages, industrial deployment of Candida species has been hindered by concerns regarding opportunistic pathogenicity and the historical lack of efficient genetic manipulation tools, leading to a substantial gap between metabolic potential and practical utilization. Recent advances in functional genomics, genome editing, and systems metabolic engineering are rapidly overcoming these barriers, enabling more precise and efficient strain development. In this review, we systematically summarize recent progress in the metabolic engineering of Candida species as microbial cell factories, with particular emphasis on expanding genetic toolkits, utilizting renewable and non-conventional carbon sources, and biosynthesizing high-value compounds. In addition, we propose a biosafety-oriented classification framework to support their safe industrial deployment. Finally, we discuss current challenges and emerging opportunities, emphasizing that the synergy of synthetic biology and artificial intelligence-driven design holds the key to unlocking the biotechnological potential of Candida yeasts.
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6. Systems metabolic engineering of Escherichia coli for high-level branched-chain fatty acid production via dual precursor pathways.
PMID:日期:2026-11-01Branched-chain fatty acids (BCFAs), naturally synthesized by Gram-positive bacteria, are promising feedstocks for the production of advanced biofuels. However, efficient BCFA biosynthesis in Gram-negative bacteria such as Escherichia coli remains challenging because of insufficient supply of branched-chain acyl-CoA precursors, poor compatibility of the endogenous fatty acid synthesis pathway with branched-chain substrates, and limited cellular robustness toward non-native fatty acids. In this study, we first engineered an orthogonal isovaleryl-CoA biosynthetic pathway in E. coli and demonstrated its functionality in supporting BCFA production. Importantly, we identified a strong synergistic interaction between the isovaleryl-CoA pathway and the branched-chain α-keto acid dehydrogenase pathway, and thereby established a dual-route strategy for precursor supply. To further enhance BCFA production, we rewired central carbon metabolism by eliminating competing pathways and introducing a non-oxidative glycolysis pathway to increase acetyl-CoA availability while minimizing byproduct formation. We additionally optimized the fatty acid biosynthetic module through expression of a highly active 'TesA (R65C) variant and the transcriptional regulator FadR, and enhanced cellular robustness via introduction of N138H mutation into PcnB and overexpression of the stress resistance associated genes rfaY and yafL. The final engineered strain produced 2.96 g/L BCFAs (approximately 10-fold higher than the previously reported titers), representing 55% of total fatty acids, with a yield of 0.08 g/g glucose. Overall, this work established a dual-precursor supply strategy combined with systems metabolic engineering for BCFA production, providing a foundation for the development of sustainable bioprocesses for advanced branched-chain biofuels.
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7. Systematic metabolic engineering of Escherichia coli for high-level production of trans-4-hydroxy-L-proline.
PMID:日期:2026-11-01As a high-value-added amino acid derivative, trans-4-hydroxy-L-proline (T-4-Hyp) faces key bottlenecks in its microbial production from glucose, including insufficient precursor supply and an imbalance between cell growth and product biosynthesis. In this study, we successfully constructed an engineered Escherichia coli strain QF-27 for efficient T-4-Hyp production. First, the L-proline (L-Pro) biosynthetic pathway was enhanced by overexpressing the feedback-resistant γ-glutamyl kinase, glutamate-γ-semialdehyde dehydrogenase, and pyrroline-5-carboxylate reductase, and by knocking out the L-proline dehydrogenase. The resulting strain QF-9 produced 15.75 ± 0.56 g/L of L-Pro. Subsequently, the expression level of proline-4-hydroxylase from Dactylosporangium sp. RH1 was optimized in strain QF-9, and the resulting strain QF-14 produced 5.32 ± 0.26 g/L of T-4-Hyp. To address the insufficient supply of α-ketoglutarate (α-KG), a multi-modular synergistic strategy (i.e., blocking byproduct pathways, enhancing α-KG flux, and relieving global transcriptional repression) increased T-4-Hyp production to 11.02 ± 0.27 g/L. Moreover, a dynamic switch combining P promoter and DAS+4 degradation tag was designed to repress expression and promote degradation of the α-ketoglutarate dehydrogenase complex during the stationary phase, thereby balancing cell growth and T-4-Hyp production. Consequently, T-4-Hyp production reached 14.37 ± 0.46 g/L, and residual L-Pro fell to 0.38 ± 0.17 g/L. In fed-batch fermentation, the final strain QF-27 produced 105.72 ± 0.84 g/L of T-4-Hyp with productivity of 2.20 g/L/h and carbon yield of 0.364 g/g glucose. To our knowledge, this is the best performance reported for T-4-Hyp production by microbial fermentation, and the first study to enhance it via systematic modification of central carbon metabolism.
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8. Discovery, identification of tricyclic sesquiterpene avermitilol synthase, and its heterologous production in plasmid-free Corynebacterium glutamicum.
8. 三环倍半萜avermitilol合酶的发现、鉴定及其在无质粒谷氨酸棒杆菌中的异源生产PMID:日期:2026-11-01[中文摘要] 三环倍半萜是一类具有生物活性的天然产物，在药物、香料和可持续航空生物燃料等领域具有广泛应用。然而，已表征的三环倍半萜合酶（tSTS）数量仍然有限。为系统性地拓展这一酶类，我们开发了一套多步骤生物信息学工作流程，用于鉴定编码环状倍半萜合酶的基因，该流程整合了基于BLAST的同源筛选、保守基序验证、基于AlphaFold2的结构建模以及分子对接。该工作流程将初始的1063个tSTS候选酶逐步精炼至6个满足C1-C10距离标准的推定酶。将全部6个候选酶在过表达甲基赤藓醇4-磷酸途径基因模块的谷氨酸棒杆菌JP-2中进行异源表达，证实了其生物合成活性，产生了5种已知的环状倍半萜以及由来自Actinokineospora terrae的tSTS（AtTPS）产生的三环avermitilol，后者通过NMR波谱和高分辨电喷雾电离质谱进行了鉴定。为提高工业可行性，将化学诱导型启动子替换为组成型无前导序列合成σ启动子，并通过GGGGS连接肽将avermitilol合酶与法尼基焦磷酸合酶融合，增强了酶间中间体的局部浓度。此外，通过CRISPR相关转座子系统构建了无质粒、无抗生素选择压力的菌株，实现了avermitilol合酶表达盒的双重染色体整合，avermitilol产量达到81.52 mg/L。染色体整合菌株在连续传代中保持稳定生产，而基于质粒的菌株则表现出超过90%的生产力损失。在2 L生物反应器中对AVM-int02cp进行补料分批发酵，最终avermitilol滴度达到100.99 mg/L。本研究通过在一个微生物宿主中鉴定一个未表征的合酶基因，展示了针对三环倍半萜的序列和三维结构辅助的从基因发现到生产的工作流程。
[英文摘要] Tricyclic sesquiterpenes are bioactive natural products with broad applications in pharmaceuticals, fragrances, and sustainable aviation biofuels. However, the repertoire of characterized tricyclic sesquiterpene synthases (tSTSs) remains limited. To systematically expand this enzyme class, we developed a multi-step bioinformatics workflow to identify genes encoding for cyclic sesquiterpene synthase integrating BLAST-based homology filtering, conserved motif validation, AlphaFold2-based structural modeling, and molecular docking. This workflow progressively refined an initial set of 1063 tSTS candidates to six putative enzymes that satisfied a C1-C10 distance criterion. Heterologous expression of all six candidates in Corynebacterium glutamicum JP-2 overexpressing a methylerythritol 4-phosphate pathway gene module confirmed biosynthetic activity, yielding five known cyclic sesquiterpenes and tricyclic avermitilol produced by a tSTS (AtTPS) identified from Actinokineospora terrae by NMR spectroscopy and high-resolution electrospray ionization mass spectrometry. To improve industrial feasibility, the chemical-inducible promoter was replaced with constitutive leaderless synthetic σ promoters, and fusion of avermitilol synthase with farnesyl pyrophosphate synthase via a GGGGS linker enhanced the local concentration of intermediates between enzymes. In addition, a plasmid-free, antibiotic selection-free strain was constructed via the CRISPR-associated transposons, enabling dual chromosomal integrations of the avermitilol synthase expression cassette and achieving 81.52 mg/L avermitilol production. The chromosomally integrated strain maintained stable production over serial passages, whereas the plasmid-based strain exhibited greater than 90% loss of productivity. Fed-batch fermentation of AVM-int02cp in a 2-L bioreactor achieved a final avermitilol titer of 100.99 mg/L. This work demonstrates a sequence- and 3D structure-assisted gene discovery-to-production workflow for a tricyclic sesquiterpene through the identification of an uncharacterized synthase gene in a microbial host.
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9. Humanization of N-glycan-dependent protein quality-control system in Kluyveromyces marxianus promotes glycoprotein secretion.
PMID:日期:2026-11-01Human N-glycoproteins represent a market worth hundreds of billions of dollars, yet their production in yeast is often limited by misfolding and degradation. However, few strategies have addressed this limitation by targeting differences between human and yeast N-glycan-dependent protein quality control (QC), including the absence of the UGGT-mediated reglucosylation-refolding cycle and the simpler glycoprotein degradation pathway in yeast. Here, we engineered the glycoprotein QC system of Kluyveromyces marxianus by introducing key human components and modifying native pathways. Human UGGT1 or UGGT2 enhanced soluble and secretory glycoprotein production in an activity-dependent manner, with further improvements achieved by co-expressing the human cochaperone SEP15 and reducing native glucosidase II trimming. Human EDEM2 delayed endoplasmic reticulum-associated degradation and increased secretion. Combining these strategies enhanced the production of diverse N-glycoproteins, including Fc, γ-glutamyl hydrolase, fungal xylanase, and Fc-fusion therapeutics, by up to ∼12-fold, demonstrating an effective strategy for engineering human-like glycoprotein QC in yeast to improve glycoprotein production.
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10. Metal ions program flavonolignan biosynthesis and enable photo-biohybrid production.
PMID:日期:2026-11-01Flavonolignans are pharmacologically important plant natural products whose production has been limited to extraction from natural sources. Their defining transformation, the oxidative coupling of flavonoid and phenylpropanoid precursors, was demonstrated to be enzyme-catalyzed. Here we show that milk thistle flavonolignans can also be assembled through an abiotic, light-driven process in vitro. Photocatalytic coupling of taxifolin and coniferyl alcohol generated the major natural flavonolignans, including silychristins, whose synthesis from native precursors has not previously been reproduced in vitro. Importantly, we identify environmental metal ions as programmable regulators of reaction outcome. Fe and Al selectively direct radical coupling toward silychristin formation, whereas Mn primarily enhances catalytic efficiency. Mechanistic analyses indicate that metal coordination of flavonoid substrates governs regioselective radical attack and molecular architecture of final products. Leveraging this principle, we establish a metal-programmable photocatalytic platform for the synthesis of both natural and new-to-nature flavonolignans. Integration of this abiotic chemistry with engineered Saccharomyces cerevisiae enabled de novo flavonolignan production directly from sugar in a one-pot photo-biohybrid process for the first time, establishing a versatile strategy for the sustainable production and diversification of flavonolignans.