Biotechnology advances最新文献_第7页

Accelerated adaptive laboratory evolution: A tool for evolutionary biotechnology 加速适应实验室进化：进化生物技术的工具。

IF 12.5 1区工程技术 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Biotechnology advances

Pub Date : 2025-10-22 DOI: 10.1016/j.biotechadv.2025.108741

Luna Declerck , Florent Bouchon , Wouter Demeester , Chiara Guidi , Marjan De Mey

Adaptive laboratory evolution (ALE) is a powerful strategy for enhancing microbial traits by harnessing the principles of natural selection in controlled environments. It has enabled significant advances in microbial growth, stress tolerance, and product yield across a variety of organisms, while also providing insight into evolutionary mechanisms. However, the traditional ALE workflow is time- and resource-intensive, relying on prolonged cultivation to allow beneficial mutations to emerge and be maintained in the population. To improve this, a range of evolutionary engineering tools have been developed to accelerate ALE by increasing mutation rates and genetic diversity in evolving strains. In this review, we explore the core parameters that shape ALE, such as selection pressure, transfer method, and passage size, and provide a comprehensive overview of both established and emerging acceleration methods. These techniques are categorized based on portability (applicability across different microorganisms), genomic targetability (specificity of mutagenesis), and reliability (minimal off-target mutations and mutational reproducibility), with the resulting framework for selecting the most suitable approach summarized in Table 3 at the end of the review. We highlight the growing potential of accelerated ALE and outline future directions, including the integration of genome-wide and targeted mutagenesis, computational modeling, laboratory automation, and broader application beyond model organisms. This review aims to streamline the use of accelerated ALE, unlocking its true potential for advancing microbial strain engineering.

适应性实验室进化（ALE）是一种在受控环境中利用自然选择原理来增强微生物特性的有力策略。它使微生物生长、抗逆性和各种生物的产品产量取得了重大进展，同时也为进化机制提供了见解。然而，传统的ALE工作流程是时间和资源密集型的，依赖于长时间的培养来允许有益的突变在种群中出现和维持。为了改善这一点，已经开发了一系列进化工程工具，通过增加进化菌株的突变率和遗传多样性来加速ALE。在这篇综述中，我们探讨了形成ALE的核心参数，如选择压力、传递方法和通道尺寸，并对现有的和新兴的加速方法进行了全面的概述。这些技术根据可移植性（在不同微生物中的适用性）、基因组靶向性（诱变的特异性）和可靠性（最小的脱靶突变和突变的可重复性）进行分类，最终选择最合适的方法的框架总结在本文最后的表3中。我们强调了加速ALE的增长潜力，并概述了未来的方向，包括全基因组和靶向诱变的整合，计算建模，实验室自动化以及模式生物以外的更广泛应用。本综述旨在简化加速ALE的使用，释放其推进微生物菌株工程的真正潜力。

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引用次数: 0

Recent advances in microbial biosynthesis of L-cysteine and its derivative sulfur-containing antioxidants l -半胱氨酸及其衍生物含硫抗氧化剂的微生物合成研究进展。

IF 12.5 1区工程技术 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Biotechnology advances

Pub Date : 2025-10-22 DOI: 10.1016/j.biotechadv.2025.108744

Hui Gao , JunJie Sun , Xian Zhang , Zhiming Rao , Meijuan Xu

Sulfur is an essential element for life, and most microorganisms are actively involved in the global sulfur cycle through sulfur oxidation and sulfate reduction pathways. Among sulfur-containing metabolites, L-cysteine plays a central role as a precursor to various thiol-based antioxidants, including glutathione, mycothiol, ergothioneine, and taurine. These compounds are critical for maintaining redox homeostasis, modulating oxidative stress responses, and mediating cellular signaling. However, the complexity of L-cysteine metabolism and the inherently low sulfur conversion efficiency present major obstacles to the large-scale biosynthesis and application of sulfur-containing antioxidants. This review provides a comprehensive overview of the sulfur assimilation ability of inorganic sulfur sources in microorganisms and summarizes the metabolic pathways and regulatory mechanisms of sulfur-containing antioxidants mediated by L-cysteine in different strains. In particular, this review focuses on the regulation of sulfur-containing antioxidants on redox balance during oxidative stress. Furthermore, we discuss their potential applications in the selection and expansion of microorganisms, the exploration and regulation of novel metabolic targets, and the coordination of carbon/sulfur modules. By coordinating the yield of target products, they can regulate the balance of oxidative and reduction pressures. These insights provide promising strategies to alleviate oxidative stress during industrial fermentation and to facilitate the development of robust microbial chassis strains.

硫是生命必需的元素，大多数微生物通过硫氧化和硫酸盐还原途径积极参与全球硫循环。在含硫代谢物中，l-半胱氨酸作为各种巯基抗氧化剂的前体起着核心作用，包括谷胱甘肽、真菌硫醇、麦角硫因和牛磺酸。这些化合物对于维持氧化还原稳态、调节氧化应激反应和介导细胞信号传导至关重要。然而，l -半胱氨酸代谢的复杂性和固有的低硫转化效率是大规模生物合成和应用含硫抗氧化剂的主要障碍。本文综述了微生物对无机硫源的硫同化能力，并对l -半胱氨酸介导的含硫抗氧化剂在不同菌株中的代谢途径和调控机制进行了综述。本文就含硫抗氧化剂对氧化应激过程中氧化还原平衡的调控作一综述。此外，我们还讨论了它们在微生物的选择和扩展、新代谢靶点的探索和调控以及碳/硫模块的协调方面的潜在应用。通过协调目标产物的产率，它们可以调节氧化和还原压力的平衡。这些见解为缓解工业发酵过程中的氧化应激提供了有希望的策略，并促进了健壮的微生物底盘菌株的发展。

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引用次数: 0

From IscB to Cas9: Engineering and advances in the next generation of miniature gene editing tools 从IscB到Cas9：下一代微型基因编辑工具的工程和进展。

IF 12.5 1区工程技术 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Biotechnology advances

Pub Date : 2025-10-20 DOI: 10.1016/j.biotechadv.2025.108743

Changli Zhou , Sisi Zhu , Chengjian Luo , Wenju Wang , Huiqin Fan , Yuan Gao , Xinde Xu , QiuYan Wang , Yu You , Tian Xie

The CRISPR-Cas system, distinguished by its inherent modularity and broad programmability, has catalyzed a paradigm shift in genome engineering due to its unprecedented accuracy, specificity, and on-target efficiency, now serving as the cornerstone of modern genome manipulation. The efficient delivery of gene editing tools remains a major technical hurdle to clinical application, primarily due to the lack of compact editors. The recent identification of the transposon-associated nuclease IscB as an evolutionary ancestor of Cas9 has provided important insights into the molecular evolution of the CRISPR–Cas9 system. Notably, IscB is a highly compact nuclease, approximately one-third the size of Cas9, capable of precise nucleic acid cleavage in eukaryotic cells under the guidance of ωRNA. These features make it a promising candidate for the development of next-generation miniaturized genome editors. However, natural IscB exhibits limited editing performance in eukaryotic systems.

This review first outlines the biochemical function of the transposon IscB and briefly traces the evolutionary origin of the Cas9 system. It then describes and compares the structural characteristics and cleavage mechanisms of OgeuIscB and Cas9. Subsequent sections summarize various engineering strategies for current IscB systems, including the development of base editors and recent advances in their application. Finally, the limitations of existing systems are discussed, and potential directions for future optimization are proposed, aiming to provide new insights and facilitate the advancement of IscB-based miniaturized editors.

CRISPR-Cas系统以其固有的模块化和广泛的可编程性而闻名，由于其前所未有的准确性、特异性和靶向效率，催化了基因组工程的范式转变，现在成为现代基因组操作的基石。基因编辑工具的有效传递仍然是临床应用的主要技术障碍，主要是由于缺乏紧凑型编辑器。最近发现转座子相关核酸酶IscB是Cas9的进化祖先，这为CRISPR-Cas9系统的分子进化提供了重要的见解。值得注意的是，IscB是一种高度紧凑的核酸酶，大小约为Cas9的三分之一，能够在ωRNA的指导下在真核细胞中精确切割核酸。这些特点使其成为开发下一代小型化基因组编辑器的一个有希望的候选者。然而，天然IscB在真核系统中表现出有限的编辑性能。本文首先概述了转座子IscB的生化功能，并简要追溯了Cas9系统的进化起源。然后描述并比较了OgeuIscB和Cas9的结构特征和裂解机制。随后的部分总结了当前IscB系统的各种工程策略，包括碱基编辑器的发展及其应用的最新进展。最后，讨论了现有系统的局限性，并提出了未来优化的潜在方向，旨在为基于iscb的小型化编辑器的发展提供新的见解。

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引用次数: 0

Innovative strategies to enhance lipid accumulation for algal biodiesel production: Ultrasound treatment, external electrostimulation, and integration of bioelectrochemical systems 提高藻类生物柴油生产中脂质积累的创新策略：超声处理、外部电刺激和生物电化学系统的集成。

IF 12.5 1区工程技术 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Biotechnology advances

Pub Date : 2025-10-17 DOI: 10.1016/j.biotechadv.2025.108740

Iryna Rusyn

Microalgae-based biodiesel, known as third-generation biodiesel, offers a promising path forward by combining efficient carbon capture with high biofuel yields. At the same time, it can address ethical and environmental concerns related to competition with food crops and habitat loss caused by oil crop cultivation, which remain critical challenges for sustainable biodiesel development. However, despite its potential, algal biodiesel production is hampered by several critical limitations, particularly the inherent trade-off between biomass accumulation and lipid synthesis, the low biomass and lipid yields, and the high costs associated with cultivation technologies and downstream processing. This study provides an in-depth review of recent advances in innovative ultrasonic and electrochemical strategies to overcome these bottlenecks into algal cultivation processes. Furthermore, our discussions have covered underlying mechanisms through which these stimuli affect algal metabolism, with the goal of gaining deeper insight into their applicability and long-term potential in sustainable biofuel production systems. The findings of this study demonstrate that ultrasound treatment, external electrostimulation, and the integration of bioelectrochemical systems represent effective tools markedly enhance microalgal biomass productivity and lipid accumulation. Optimization of treatment regimes and their synergistic interaction with other factors provides a robust approach to concurrently stimulating both algal growth and lipid biosynthesis. Additionally, these approaches also streamline downstream processing by improving lipid extraction efficiency, reducing reaction time, minimizing chemical input, and decreasing the number of processing stages. The compatibility of these technologies with waste-based cultivation and remediation further enhances their sustainability profile while simultaneously reducing operational costs on aeration demand, and CO₂ supplementation requirements. Representing promising frontiers in the field, these emerging and insufficiently studied approaches offer both environmental and economic advantages and warrant intensified research efforts to fully unlock their potential for advancing sustainable algal biofuel production.

以微藻为基础的生物柴油，被称为第三代生物柴油，通过将高效的碳捕获与高生物燃料产量相结合，提供了一条有前途的发展道路。与此同时，它可以解决与粮食作物竞争和油料作物种植造成的栖息地丧失有关的伦理和环境问题，这些问题仍然是可持续生物柴油发展的关键挑战。然而，尽管有潜力，藻类生物柴油的生产受到几个关键限制的阻碍，特别是生物质积累和脂质合成之间的内在权衡，低生物量和脂质产量，以及与培养技术和下游加工相关的高成本。本研究深入回顾了近年来在创新超声和电化学策略方面的进展，以克服藻类培养过程中的这些瓶颈。此外，我们的讨论涵盖了这些刺激影响藻类代谢的潜在机制，目的是更深入地了解它们在可持续生物燃料生产系统中的适用性和长期潜力。本研究结果表明，超声处理、外部电刺激和生物电化学系统的整合是有效的工具，可显著提高微藻生物量生产力和脂质积累。优化处理方案及其与其他因素的协同作用为同时刺激藻类生长和脂质生物合成提供了一种强有力的方法。此外，这些方法还通过提高脂质提取效率、缩短反应时间、减少化学投入和减少处理阶段数量来简化下游加工。这些技术与基于废物的种植和修复的兼容性进一步提高了其可持续性，同时降低了曝气需求和CO₂补充需求的运营成本。这些新兴的、尚未得到充分研究的方法代表了该领域前景广阔的前沿，提供了环境和经济优势，需要加强研究工作，以充分释放其推进可持续藻类生物燃料生产的潜力。

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引用次数: 0

Material-binding peptides: sources, mechanisms, directed evolution and applications 物质结合肽：来源、机制、定向进化和应用。

IF 12.5 1区工程技术 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Biotechnology advances

Pub Date : 2025-10-16 DOI: 10.1016/j.biotechadv.2025.108742

Huan Chen , Ya-Ting Gao , Xu-Zhe Ge , Xin Wang , Feng Cheng , Ya-Ping Xue , Yu-Guo Zheng

Material-binding peptides (MBPs) can specifically bind to materials under mild conditions, such as room temperature and aqueous environments, thereby offering promising applications in both biotechnology and materials science. Recent advances in screening techniques, including phage display, bacterial display, and proteomics-based methods, combined with innovations in protein engineering and machine learning, have significantly accelerated the discovery and optimization of MBPs. These peptides have been successfully applied in areas such as catalyst immobilization (biocatalysis), biodegradation, and biomimetic mineralization. This review provides a comprehensive synthesis of the state-of-the-art in MBP research. It begins by discussing the sources of MBPs and the engineering strategies used to enhance their performance, then delves into the molecular mechanisms underlying their material interactions, and finally examines their emerging industrial applications. The review aims to guide researchers through current screening methodologies, provide mechanistic insights, and explore practical applications, offering a roadmap for future advancements in the field.

材料结合肽（MBPs）可以在室温和水环境等温和条件下特异性结合材料，因此在生物技术和材料科学中都有很好的应用前景。筛选技术的最新进展，包括噬菌体展示、细菌展示和基于蛋白质组学的方法，结合蛋白质工程和机器学习的创新，极大地加速了MBPs的发现和优化。这些多肽已成功应用于催化剂固定化（生物催化）、生物降解和仿生矿化等领域。本文综述了MBP研究的最新进展。首先讨论MBPs的来源和用于提高其性能的工程策略，然后深入研究其材料相互作用的分子机制，最后研究其新兴的工业应用。该综述旨在指导研究人员了解当前的筛选方法，提供机制见解，并探索实际应用，为该领域的未来发展提供路线图。

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引用次数: 0

Smart culture medium optimization for recombinant protein production: Experimental, modeling, and AI/ML-driven strategies 重组蛋白生产的智能培养基优化：实验、建模和AI/ ml驱动策略。

IF 12.5 1区工程技术 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Biotechnology advances

Pub Date : 2025-10-15 DOI: 10.1016/j.biotechadv.2025.108738

Galib Khan , Carrie Sanford , Cong T. Trinh

Recombinant protein production (RPP) is central to biotechnology, where recombinant proteins are used as either end products or catalysts in the synthesis of chemicals, fuels, and materials. Among the major cost drivers, culture medium plays a pivotal role in determining protein yield and quality. This review presents a comprehensive perspective on the critical stages of “smart” culture medium optimization: planning, screening, modeling, optimization, and validation. In the planning stage, we examine the nutritional and energetic roles of medium components, including carbon, nitrogen, amino acids, salts, and trace metals, and their impacts on culture parameters such as pH, oxidative state, and osmolality. We highlight the variability in trace metal content due to water sources, culture vessels, and raw materials, which can substantially influence RPP. The screening stage covers Design of Experiments (DoE) approaches, assessing their theoretical basis, implementation, and limitations. For modeling, we describe methods that integrate experimental data to develop predictive models for smart medium formulation. Model-based optimization strategies can then be employed to select optimal media compositions for a given application. The validation stage aims to evaluate model predictions and provide feedback for model training and refinement. Finally, we survey mechanistic and artificial intelligence/machine learning (AI/ML)-driven models as integrated, transformational tools for predictive modeling of bioprocess conditions, nutrient availability, cellular metabolism, and protein quality, with the goal of optimizing culture media to enhance protein yields while reducing costs and environmental impact. We conclude by addressing the challenges of translating laboratory-scale medium optimization to industrial-scale settings and exploring future AI/ML-driven approaches that may overcome current bottlenecks and accelerate medium design for RPP. Overall, this review provides a unified framework for advancing smart medium design in RPP.

重组蛋白生产（RPP）是生物技术的核心，重组蛋白被用作合成化学品、燃料和材料的最终产品或催化剂。在主要的成本驱动因素中，培养基在决定蛋白质产量和质量方面起着关键作用。本文综述了“智能”培养基优化的关键阶段：规划、筛选、建模、优化和验证。在计划阶段，我们研究了培养基成分的营养和能量作用，包括碳、氮、氨基酸、盐和微量金属，以及它们对pH、氧化状态和渗透压等培养参数的影响。我们强调了由于水源、培养容器和原材料而引起的微量金属含量的变化，这些变化会极大地影响RPP。筛选阶段包括实验设计（DoE）方法，评估其理论基础，实施和局限性。对于建模，我们描述了整合实验数据以开发智能介质配方预测模型的方法。然后可以使用基于模型的优化策略为给定的应用程序选择最佳的媒体组合。验证阶段的目的是评估模型预测，并为模型训练和改进提供反馈。最后，我们调查了机械和人工智能/机器学习（AI/ML）驱动的模型，作为生物过程条件、营养可用性、细胞代谢和蛋白质质量预测建模的集成转换工具，目的是优化培养基，提高蛋白质产量，同时降低成本和环境影响。最后，我们解决了将实验室规模的介质优化转化为工业规模设置的挑战，并探索了未来人工智能/机器学习驱动的方法，这些方法可能克服当前的瓶颈，并加速RPP的介质设计。总之，这篇综述为推进RPP中的智能介质设计提供了一个统一的框架。

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引用次数: 0

Circular RNAs in microalgae: Uncovering their biological significance 微藻中的环状rna：揭示其生物学意义。

IF 12.5 1区工程技术 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Biotechnology advances

Pub Date : 2025-10-15 DOI: 10.1016/j.biotechadv.2025.108739

Jaber Dehghani , Bahman Panahi , Jens Mortansson Jelstrup Nolsøe , Patrice Lerouge , Muriel Bardor , Yadollah Omidi

Circular RNAs (circRNAs) have recently garnered significant attention due to their emerging regulatory roles across eukaryotic organisms. These non-coding RNA molecules are generated through a non-canonical back-splicing mechanism that covalently joins the 5′ and 3′ ends, resulting in a closed-loop structure. Although the complete functional landscape of circRNAs remains to be elucidated, advances in RNA sequencing technologies and computational biology have accelerated their identification and functional annotation in both plant and mammalian systems. CircRNAs are increasingly implicated in the regulation of key cellular and metabolic processes, including transcription, translation, protein-protein interactions, cellular proliferation, development, and stress responses, thereby contributing to homeostasis and survival. In this study, we present a comprehensive overview of circRNA biogenesis, structural features, biological roles, and bioinformatic tools used for their prediction in eukaryotes. However, no prior studies have systematically characterized circRNAs in microalgae. To address this gap, we analyzed RNA-seq datasets from three phylogenetically distinct microalgal species (e.g., Chlamydomonas reinhardtii, Dunaliella salina, and Phaeodactylum tricornutum) using the CIRI2 pipeline to identify putative circRNAs. Our analysis revealed candidate circRNAs potentially involved in essential biological pathways, including RNA transcription regulation, mRNA splicing, translational control, chlorophyll function, cytochrome c maintenance, and various post-transcriptional and post-translational modifications. These findings offer novel insights into the regulatory landscape of circRNAs in microalgal species and lay the groundwork for future functional investigations.

环状rna （circRNAs）最近因其在真核生物中的新兴调控作用而引起了极大的关注。这些非编码RNA分子是通过非规范的反向剪接机制产生的，该机制将5‘和3’端共价连接，形成闭环结构。尽管环状RNA的完整功能景观仍有待阐明，但RNA测序技术和计算生物学的进步已经加速了它们在植物和哺乳动物系统中的鉴定和功能注释。CircRNAs越来越多地参与关键细胞和代谢过程的调控，包括转录、翻译、蛋白-蛋白相互作用、细胞增殖、发育和应激反应，从而有助于体内平衡和生存。在这项研究中，我们全面概述了真核生物中circRNA的生物发生、结构特征、生物学作用以及用于预测circRNA的生物信息学工具。然而，之前没有研究系统地表征微藻中的环状rna。为了解决这一空白，我们使用CIRI2管道分析了来自三种不同系统发育的微藻物种（如莱因哈衣藻、盐藻Dunaliella salina和三角褐藻Phaeodactylum tricornutum）的RNA-seq数据集，以鉴定推测的环状rna。我们的分析揭示了候选环状RNA可能参与必要的生物学途径，包括RNA转录调控、mRNA剪接、翻译控制、叶绿素功能、细胞色素c维持以及各种转录后和翻译后修饰。这些发现为微藻物种中环状rna的调控格局提供了新的见解，并为未来的功能研究奠定了基础。

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引用次数: 0

Exploring the enzymatic landscape of 4-α-glucanotransferases in carbohydrate bioprocessing 探索碳水化合物生物加工中4-α-葡萄糖基转移酶的酶景观。

IF 12.5 1区工程技术 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Biotechnology advances

Pub Date : 2025-10-14 DOI: 10.1016/j.biotechadv.2025.108737

Yu Wang , Yu Tian , Marie Sofie Møller , Zhengyu Jin , Xiaoxiao Li , Birte Svensson

4-α-Glucanotransferases (4αGTs), also known as amylomaltases or disproportionating enzymes, catalyze α-1,4-glucan and maltooligosaccharide transfer in starch and glycogen metabolism of microorganisms, plants and animals. The present review covers their classification, reactions, structure-function relationships, engineering and applications. 4αGTs belong to glycoside hydrolase families GH13, GH57, and GH77, and catalyze four types of reactions: disproportionation, cyclization, coupling, and hydrolysis, of which the first two are particularly important for biotechnological applications. Insights into active site structures and substrate binding have facilitated the rational design of product specificity, modes of action, and increased product yields. Assays of the four reactions encompass monitoring amylose consumption by iodine staining, release of glucose in maltotriose disproportionation, chromatographic analysis of change in chain lengths, and release of reducing sugar by hydrolysis. Major reactions in transglycosylation of starch include formation of amylopectin with extended branch chains and cyclization to large-ring cyclodextrins (LR-CDs), also referred to as cycloamyloses (CAs). Product yields, chain length distribution, and size of LR-CDs depend on the enzyme, substrates and reaction conditions. 4αGT products are useful in the food, biomaterials and pharma sectors. Thus, chain length modification can elicit resistance of starch to digestion via structural reorganization and confer thermo-reversible gel formation, while LR-CDs can increase aqueous solubility of guest-molecules for controlled delivery and adjust rheological behavior of starches. Moreover, 4αGT can generate bioactive glycoconjugates and novel oligosaccharides by transglycosylation. Future development of 4αGT-catalyzed reactions includes optimization by rational enzyme engineering and high-throughput screening technologies. This review portrays the immense potential of 4αGTs in sustainable biomanufacturing.

4-α-葡聚糖转移酶（4α gts），又称淀粉酶或歧化酶，在微生物、植物和动物的淀粉和糖原代谢中催化α-1,4-葡聚糖和麦芽糖低聚糖的转移。综述了它们的分类、反应、构效关系、工程及应用。4α gt属于糖苷水解酶家族GH13、GH57和GH77，可催化歧化、环化、偶联和水解四种反应，其中前两种反应在生物技术应用中尤为重要。对活性位点结构和底物结合的深入了解有助于合理设计产品特异性、作用模式和提高产品产量。这四种反应的测定包括用碘染色法监测直链淀粉的消耗、麦芽糖歧化过程中葡萄糖的释放、链长变化的色谱分析以及水解释放还原糖。淀粉转糖基化的主要反应包括支链延长的支链淀粉的形成和环化成大环环糊精（LR-CDs），也被称为环直链淀粉（CAs）。产物产率、链长分布和LR-CDs的大小取决于酶、底物和反应条件。4αGT产品在食品、生物材料和制药领域都很有用。因此，链长修饰可以通过结构重组引起淀粉对消化的抗性，并赋予热可逆凝胶形成，而LR-CDs可以增加客体分子的水溶性，以控制递送并调节淀粉的流变行为。此外，4αGT可以通过转糖基化生成具有生物活性的糖缀合物和新型低聚糖。4α gt催化反应的未来发展包括合理的酶工程优化和高通量筛选技术。这篇综述描绘了4α gt在可持续生物制造中的巨大潜力。

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引用次数: 0

Decoding bioprocesses with transcriptomics: current status and future potential 用转录组学解码生物过程：现状和未来潜力。

IF 12.5 1区工程技术 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Biotechnology advances

Pub Date : 2025-10-13 DOI: 10.1016/j.biotechadv.2025.108736

Nadja Alina Henke , Boas Pucker , Alexander Grünberger

Transcriptomic analyses represent widely used state-of-the art methodologies in molecular biosciences going back to the early 1960s. Over the last years, transcriptomics has become increasingly important in the field of bioprocess engineering. Systematic transcriptomics platform technologies (especially RNA-seq) play an accelerating role to investigate the gene expression profiles of cells in diverse bioprocesses, covering prokaryotic and eukaryotic cell systems. This review summarizes how different transcriptomics methodologies from RT-qPCR to microarrays and RNA-seq have been applied in bioprocess engineering to date. The major scopes of the reviewed works can be categorized as the following: strain/cell line characterization, investigation of culture/media conditions, process operations as well as scale-up/down studies. Subsequently, a perspective is given how emerging sequencing-based transcriptomics could envision the understanding of population diversities in space and time aided by single cell analysis (scRNA-seq) as well as transcriptional histories (Record-Seq).

转录组学分析代表了分子生物科学中广泛使用的最新方法，可以追溯到20世纪60年代初。在过去的几年里，转录组学在生物过程工程领域变得越来越重要。系统转录组学平台技术（特别是RNA-seq）在研究多种生物过程中细胞的基因表达谱方面发挥着加速作用，涵盖了原核和真核细胞系统。本文综述了迄今为止从RT-qPCR到微阵列和RNA-seq等不同的转录组学方法在生物工艺工程中的应用。所审查的工作的主要范围可分为以下几类：菌株/细胞系特性、培养/培养基条件调查、工艺操作以及放大/缩小研究。随后，给出了新兴的基于测序的转录组学如何在单细胞分析（scRNA-seq）和转录历史（Record-Seq）的帮助下，设想对空间和时间上种群多样性的理解。

引用次数: 0

Decoding microbial interactions: Interaction networks and regulatory strategies for medium-chain fatty acid biosynthesis through anaerobic chain elongation 解码微生物相互作用：通过厌氧链延伸的中链脂肪酸生物合成的相互作用网络和调节策略。

IF 12.5 1区工程技术 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Biotechnology advances

Pub Date : 2025-10-12 DOI: 10.1016/j.biotechadv.2025.108735

Yi Liang, Jiadong Yu , Zonglu Yao, Yuxuan Sun, Jing Feng, Ruixia Shen, Juan Luo, Lixin Zhao

The anaerobic biosynthesis of medium-chain fatty acids (MCFAs) as valorized bio-based chemicals relies on intricate and dynamic interaction networks within microbial communities. This review systematically summarizes the key mechanisms and regulatory strategies driving MCFA biosynthesis in terms of microbial interactions, with a focus on electron donor-acceptor generation and chain elongation (CE) processes. The functional stability and resilience of anaerobic fermentation systems are collectively sustained by microbial diversity via modular functional partitioning, metabolic complementarity, resilience against perturbations, and environmental adaptation. Notably, substrate competition and syntrophic symbiosis between functional taxa directly govern the directionality and efficiency of the metabolic flux. Carbon source preferences and environmental factors synergistically steer pathway selection, while exogenous interventions such as enhanced electron transfer or niche occupation optimize microbial cooperation. In addition, quorum sensing and electrochemical synergy further balance inter-species competition to achieve a dynamic equilibrium between metabolic branch inhibition and enrichment of CE consortia. These multidimensional interaction mechanisms provide high-purity electron donors and stable metabolic foundations for MCFA synthesis to guide directional microbial engineering strategies to enhance product yields. This study systematically summarized how microbial interaction networks drive efficient MCFA biosynthesis via a multi-scale coordination between various mechanisms, including metabolic flux partitioning control, environmental response feedback, and functional modularization design, providing a theoretical foundation for resolving critical challenges during anaerobic MCFA fermentation.

中链脂肪酸（MCFAs）作为生物基化学物的厌氧生物合成依赖于微生物群落内复杂和动态的相互作用网络。本文从微生物相互作用的角度系统地总结了MCFA生物合成的关键机制和调控策略，重点介绍了电子供体-受体生成和链延伸（CE）过程。厌氧发酵系统的功能稳定性和弹性是由微生物多样性通过模块化功能分配、代谢互补、对扰动的弹性和环境适应来共同维持的。值得注意的是，功能类群之间的底物竞争和共生关系直接决定了代谢通量的方向性和效率。碳源偏好和环境因素协同引导途径选择，而外源干预如增强电子转移或生态位占据优化微生物合作。此外，群体感应和电化学协同进一步平衡了种间竞争，实现了代谢分支抑制与CE联合体富集之间的动态平衡。这些多维相互作用机制为MCFA合成提供了高纯度的电子供体和稳定的代谢基础，指导定向微生物工程策略以提高产品收率。本研究系统总结了微生物相互作用网络如何通过代谢通量分配控制、环境响应反馈和功能模块化设计等多种机制之间的多尺度协调，推动高效的MCFA生物合成，为解决厌氧MCFA发酵过程中的关键挑战提供理论基础。

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引用次数: 0