Pub Date : 2026-01-06DOI: 10.1016/j.biotechadv.2026.108797
Bishuang Chen , Yongyi Zeng , Jiangtao Sha , Huanhuan Li , Yunhan Zhang , Lan Liu , Wuyuan Zhang
Vanadium-dependent haloperoxidases (VHPOs) represent a distinct class of halogenating enzymes that catalyze the oxidation of halide ions into hypohalous acids using hydrogen peroxide and a redox-stable vanadate cofactor. In recent years, VHPOs have gained considerable attention in synthetic community due to their exceptional operational robustness, broad substrate tolerance, and particularly, the potential in driving green halo-compound synthesis. The rapid progress using VHPOs in organic synthesis inspires this review covering VHPOs discovery, structure-function insights, mechanistic elucidation, and various synthetic applications. Special attention is given to recent breakthroughs in understanding the halide and substrate specificity of VHPOs, including the identification of substrate-access tunnels and enzyme-bound halogenation mechanisms. These findings not only challenge the long-standing diffusible HOX model but also enable rational enzyme engineering. VHPOs are emerging as powerful tools for selective halogenation and sustainable synthesis, with promising prospects in synthetic biology, materials science, and environmental biotechnology.
{"title":"Vanadium-dependent haloperoxidases: Recent advances and perspectives","authors":"Bishuang Chen , Yongyi Zeng , Jiangtao Sha , Huanhuan Li , Yunhan Zhang , Lan Liu , Wuyuan Zhang","doi":"10.1016/j.biotechadv.2026.108797","DOIUrl":"10.1016/j.biotechadv.2026.108797","url":null,"abstract":"<div><div>Vanadium-dependent haloperoxidases (VHPOs) represent a distinct class of halogenating enzymes that catalyze the oxidation of halide ions into hypohalous acids using hydrogen peroxide and a redox-stable vanadate cofactor. In recent years, VHPOs have gained considerable attention in synthetic community due to their exceptional operational robustness, broad substrate tolerance, and particularly, the potential in driving green halo-compound synthesis. The rapid progress using VHPOs in organic synthesis inspires this review covering VHPOs discovery, structure-function insights, mechanistic elucidation, and various synthetic applications. Special attention is given to recent breakthroughs in understanding the halide and substrate specificity of VHPOs, including the identification of substrate-access tunnels and enzyme-bound halogenation mechanisms. These findings not only challenge the long-standing diffusible HOX model but also enable rational enzyme engineering. VHPOs are emerging as powerful tools for selective halogenation and sustainable synthesis, with promising prospects in synthetic biology, materials science, and environmental biotechnology.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108797"},"PeriodicalIF":12.5,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145921095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pathogenic plant diseases pose a serious risk to global food supplies and to the sustainable development of agriculture and forestry. Conventional control strategies, which rely heavily on chemical treatments, can disrupt ecological balance and may also affect human health. There is therefore a strong need for environmentally benign and efficient technologies that can detect disease at an early stage. This review surveys recent advances and remaining challenges in sensor based early detection of plant diseases, following the path from basic concepts to practical deployment. It first considers the biological traits and infection processes of major pathogens and identifies characteristic signaling molecules released by infected plants, which serve as design cues for sensing platforms. Existing detection strategies are then grouped into two broad categories. Direct approaches aim at the pathogen itself and use optical or electrochemical biosensors that incorporate antibodies or DNA probes. Indirect approaches focus on plant responses to stress and monitor indicators such as trace volatile organic compounds (VOCs), low frequency acoustic signals and changes in plant phenotype. Finally, the review summarizes the main classes of sensors, discusses their current limitations and outlines possible routes for technological translation and future development. Grounded in plant pathology and early disease monitoring, the review aims to provide researchers and practitioners with both an overview of the field and practical guidance for further work.
{"title":"Sensing for early-stage plant disease: From pathogenesis to sensor design","authors":"Junfeng Xie, Wenxuan Xu, Ranhua Xiong, Chaobo Huang, Miaomiao Zhu","doi":"10.1016/j.biotechadv.2026.108798","DOIUrl":"10.1016/j.biotechadv.2026.108798","url":null,"abstract":"<div><div>Pathogenic plant diseases pose a serious risk to global food supplies and to the sustainable development of agriculture and forestry. Conventional control strategies, which rely heavily on chemical treatments, can disrupt ecological balance and may also affect human health. There is therefore a strong need for environmentally benign and efficient technologies that can detect disease at an early stage. This review surveys recent advances and remaining challenges in sensor based early detection of plant diseases, following the path from basic concepts to practical deployment. It first considers the biological traits and infection processes of major pathogens and identifies characteristic signaling molecules released by infected plants, which serve as design cues for sensing platforms. Existing detection strategies are then grouped into two broad categories. Direct approaches aim at the pathogen itself and use optical or electrochemical biosensors that incorporate antibodies or DNA probes. Indirect approaches focus on plant responses to stress and monitor indicators such as trace volatile organic compounds (VOCs), low frequency acoustic signals and changes in plant phenotype. Finally, the review summarizes the main classes of sensors, discusses their current limitations and outlines possible routes for technological translation and future development. Grounded in plant pathology and early disease monitoring, the review aims to provide researchers and practitioners with both an overview of the field and practical guidance for further work.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108798"},"PeriodicalIF":12.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145902703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-04DOI: 10.1016/j.biotechadv.2026.108796
Zhiwei Pu , Xue Wang , Yihan Chen , Jishan Li , Xinxin He , Weichao Chen , Chao Zhao
Microalgae are natural and sustainable biological resources rich in high-value nutrients such as lipids, proteins, and functional pigments, which show great potential in the fields of functional foods, dietary supplements, and natural colorants. However, the yields of target components in natural microalgae are often insufficient to meet commercialization demands. The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) gene editing system, a revolutionary technology, provides a precise and effective means for targeted improvement of microalgae to enhance their nutritional value and yields. This review first outlines the basic principles of the CRISPR/Cas9 system, including its core components and gene editing mechanism. It then summarizes the application of this technology in microalgae, focusing on successful cases of modifying metabolic pathways to enrich specific nutrients, such as increasing the unsaturated fatty acid content of lipids, increasing the proportion of edible proteins, and enriching natural pigments with antioxidant properties. In addition, this review discusses the main challenges faced when applying this technology to microalgae, including delivery difficulties due to strong cell walls, low efficiency of genetic transformation, and the risk of off-target effects. Finally, the paper describes cutting-edge strategies to address these challenges, such as the development of high-fidelity Cas9 enzymes and the optimization of a single-guide RNA (sgRNA) design. Continued advances in these technologies are propelling microalgae into efficient and sustainable “cell factories”, providing the food industry with more natural, healthy, and high-value functional ingredients.
微藻是富含脂质、蛋白质、功能色素等高价值营养物质的天然可持续生物资源，在功能食品、膳食补充剂、天然着色剂等领域具有广阔的应用前景。然而，天然微藻中目标组分的产率往往不足以满足商业化需求。聚类规则间隔短回文数重复序列/CRISPR-associated protein 9 （CRISPR/Cas9）基因编辑系统是一项革命性技术，为微藻的靶向改良提供了精确有效的手段，提高微藻的营养价值和产量。本文首先概述了CRISPR/Cas9系统的基本原理，包括其核心组成部分和基因编辑机制。总结了该技术在微藻中的应用，重点介绍了通过改变代谢途径来丰富特定营养物质的成功案例，如提高脂质中不饱和脂肪酸的含量、提高可食用蛋白质的比例、丰富具有抗氧化特性的天然色素等。此外，本文还讨论了将该技术应用于微藻所面临的主要挑战，包括由于细胞壁较强而导致的递送困难、遗传转化效率低以及脱靶效应的风险。最后，本文介绍了解决这些挑战的前沿策略，如高保真Cas9酶的开发和单导RNA （sgRNA）设计的优化。这些技术的不断进步正在推动微藻成为高效和可持续的“细胞工厂”，为食品工业提供更多天然、健康和高价值的功能成分。
{"title":"Application of CRISPR/Cas9 gene editing system in microalgal metabolic engineering and synthetic strategies of functional food ingredients","authors":"Zhiwei Pu , Xue Wang , Yihan Chen , Jishan Li , Xinxin He , Weichao Chen , Chao Zhao","doi":"10.1016/j.biotechadv.2026.108796","DOIUrl":"10.1016/j.biotechadv.2026.108796","url":null,"abstract":"<div><div>Microalgae are natural and sustainable biological resources rich in high-value nutrients such as lipids, proteins, and functional pigments, which show great potential in the fields of functional foods, dietary supplements, and natural colorants. However, the yields of target components in natural microalgae are often insufficient to meet commercialization demands. The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) gene editing system, a revolutionary technology, provides a precise and effective means for targeted improvement of microalgae to enhance their nutritional value and yields. This review first outlines the basic principles of the CRISPR/Cas9 system, including its core components and gene editing mechanism. It then summarizes the application of this technology in microalgae, focusing on successful cases of modifying metabolic pathways to enrich specific nutrients, such as increasing the unsaturated fatty acid content of lipids, increasing the proportion of edible proteins, and enriching natural pigments with antioxidant properties. In addition, this review discusses the main challenges faced when applying this technology to microalgae, including delivery difficulties due to strong cell walls, low efficiency of genetic transformation, and the risk of off-target effects. Finally, the paper describes cutting-edge strategies to address these challenges, such as the development of high-fidelity Cas9 enzymes and the optimization of a single-guide RNA (sgRNA) design. Continued advances in these technologies are propelling microalgae into efficient and sustainable “cell factories”, providing the food industry with more natural, healthy, and high-value functional ingredients.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108796"},"PeriodicalIF":12.5,"publicationDate":"2026-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145894426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Methane is one of the most prominent greenhouse gases contributing to global warming. It is also a valuable source of energy and a raw material for the production of chemicals. Gas-to-liquid technologies for its conversion into methanol are particularly interesting, methanol being considered as a platform molecule for the chemical industry and a prospective fuel for low-emission transport. Methane oxidation into methanol is up to day carried out industrially under energy-consuming conditions, associated to significant CO2 emissions. Methanotrophic catalysis has arisen as a promising greener alternative since methanotrophs are naturally-occurring microorganisms (bacteria and archaea) able to uptake methane under mild conditions. Methanotrophic bacteria express the Methane MonoOxygenase (MMO) enzyme, able to selectively hydroxylate methane. However, their large-scale implementation is currently hindered by both biological and process constraints. This review summarizes recent developments in bioprocesses for methanol production from methane, including methanotroph-based ones. Whole-cell methanotrophs, cell-free (enzymatic) processes and MMO heterologous expression have been covered.
{"title":"Methane conversion into methanol by biotechnological processes: Challenges and perspectives","authors":"Héloïse Baldo , Stéphane Sauvagère , Christian Siatka , Laurence Soussan","doi":"10.1016/j.biotechadv.2026.108795","DOIUrl":"10.1016/j.biotechadv.2026.108795","url":null,"abstract":"<div><div>Methane is one of the most prominent greenhouse gases contributing to global warming. It is also a valuable source of energy and a raw material for the production of chemicals. Gas-to-liquid technologies for its conversion into methanol are particularly interesting, methanol being considered as a platform molecule for the chemical industry and a prospective fuel for low-emission transport. Methane oxidation into methanol is up to day carried out industrially under energy-consuming conditions, associated to significant CO<sub>2</sub> emissions. Methanotrophic catalysis has arisen as a promising greener alternative since methanotrophs are naturally-occurring microorganisms (bacteria and archaea) able to uptake methane under mild conditions. Methanotrophic bacteria express the Methane MonoOxygenase (MMO) enzyme, able to selectively hydroxylate methane. However, their large-scale implementation is currently hindered by both biological and process constraints. This review summarizes recent developments in bioprocesses for methanol production from methane, including methanotroph-based ones. Whole-cell methanotrophs, cell-free (enzymatic) processes and MMO heterologous expression have been covered.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108795"},"PeriodicalIF":12.5,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145894427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-29DOI: 10.1016/j.biotechadv.2025.108792
Peng-Cheng Hu , La-Mei Ding , Qiao-Qin Zhao , Mao-Cheng Tang , Pei-Fang Xiao , Chong Wang , Xiang-Yang Lu , Yun Tian , Hu-Hu Liu
Squalene, as a natural triterpenoid exhibiting various physiological activities, is primarily extracted from shark liver oil. However, due to the declining shark populations and conservation concerns, the alternative methods for squalene production are needed. Synthetic biology offers the strategies for engineered yeasts capable of producing squalene. Although the extensive studies have been performed on squalene production by the engineered yeasts, a comprehensive systematic review summarizing these efforts is lack ing. Herein, firstly, this review describes the characteristics of the squalene biosynthesis pathway in yeast cells. Secondly, metabolic strategies for enhancing squalene production in yeasts are summarized. Thirdly, the advanced genetic engineering tools to boost squalene and other terpenoids production are investigated. Fourthly, the potential of emerging other yeasts for squalene synthesis is explored. Finally, the potential technologies applied in yeasts for improving squalene production are discussed. This review will provide comprehensive information on yeasts as chassis for squalene production, laying the foundation for squalene production in yeasts.
{"title":"A review on squalene production by engineered yeasts: Current advances and perspectives","authors":"Peng-Cheng Hu , La-Mei Ding , Qiao-Qin Zhao , Mao-Cheng Tang , Pei-Fang Xiao , Chong Wang , Xiang-Yang Lu , Yun Tian , Hu-Hu Liu","doi":"10.1016/j.biotechadv.2025.108792","DOIUrl":"10.1016/j.biotechadv.2025.108792","url":null,"abstract":"<div><div>Squalene, as a natural triterpenoid exhibiting various physiological activities, is primarily extracted from shark liver oil. However, due to the declining shark populations and conservation concerns, the alternative methods for squalene production are needed. Synthetic biology offers the strategies for engineered yeasts capable of producing squalene. Although the extensive studies have been performed on squalene production by the engineered yeasts, a comprehensive systematic review summarizing these efforts is lack ing. Herein, firstly, this review describes the characteristics of the squalene biosynthesis pathway in yeast cells. Secondly, metabolic strategies for enhancing squalene production in yeasts are summarized. Thirdly, the advanced genetic engineering tools to boost squalene and other terpenoids production are investigated. Fourthly, the potential of emerging other yeasts for squalene synthesis is explored. Finally, the potential technologies applied in yeasts for improving squalene production are discussed. This review will provide comprehensive information on yeasts as chassis for squalene production, laying the foundation for squalene production in yeasts.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108792"},"PeriodicalIF":12.5,"publicationDate":"2025-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145877552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-29DOI: 10.1016/j.biotechadv.2025.108794
Shaoru Hu , Shenglong Wang , Ziyi Zhao , Yichen Wu , Ziyao Zheng , Xiang Ma , Jun Li , Mingfeng Cao , Hao Liu , Weixia Gao
Human milk oligosaccharides (HMOs) are complex carbohydrates crucial for infant nutrition, with lacto-N-neotetraose (LNnT) being a key acetylated component that makes up about 10 % of total HMOs. The synthesis of LNnT involves a sequential enzymatic process that modifies lactose, facilitated by β-1,3-N-acetylglucosaminyltransferase (β3GNT) and β-1,4-galactosyltransferase (β4GalT) using UDP-GlcNAc and UDP-Gal as substrates. This review highlights significant advancements in microbial LNnT production, focusing on two main areas: (1) innovations in enzyme engineering that improve glycosyltransferase activity and specificity through computational redesign and directed evolution; (2) strategies for optimizing metabolic flux to balance precursors using modular pathways and transporter controls. Ongoing challenges include enhancing glycosyltransferase specificity to reduce unwanted reactions and managing the complex regulatory networks of precursor flow. New approaches that utilize enzyme design for better catalytic efficiency and adaptive pathway control in response to metabolic changes appear promising for large-scale food additive production. By combining these advancements with GRAS-certified microbial platforms, future bioprocesses can tackle economic challenges while adhering to strict food safety regulations. This overview highlights the need to advance LNnT production from experimental stages to reliable, cost-effective bioprocessing systems that meet the needs of the global food industry.
人乳寡糖（HMOs）是对婴儿营养至关重要的复合碳水化合物，其中乳-n -新四糖（LNnT）是一种关键的乙酰化成分，约占总HMOs的10. %。LNnT的合成涉及一个连续的酶促过程，该过程由β-1,3- n -乙酰氨基葡萄糖转移酶（β3GNT）和β-1,4-半乳糖转移酶（β4GalT）促进，以UDP-GlcNAc和UDP-Gal为底物。本文综述了微生物LNnT生产的重大进展，重点关注两个主要领域：(1)酶工程的创新，通过计算重新设计和定向进化提高糖基转移酶的活性和特异性；(2)利用模块化途径和转运体控制优化代谢通量以平衡前体的策略。目前的挑战包括提高糖基转移酶的特异性，以减少不必要的反应和管理复杂的前体流动调节网络。利用酶设计来提高催化效率和自适应途径控制以响应代谢变化的新方法对于大规模食品添加剂生产似乎很有希望。通过将这些进步与gras认证的微生物平台相结合，未来的生物工艺可以在遵守严格的食品安全法规的同时应对经济挑战。本综述强调需要将LNnT生产从实验阶段推进到可靠的、具有成本效益的生物处理系统，以满足全球食品工业的需求。
{"title":"Metabolic engineering strategies for enhanced microbial synthesis of lacto-N-neotetraose: a key acetylated human milk oligosaccharide","authors":"Shaoru Hu , Shenglong Wang , Ziyi Zhao , Yichen Wu , Ziyao Zheng , Xiang Ma , Jun Li , Mingfeng Cao , Hao Liu , Weixia Gao","doi":"10.1016/j.biotechadv.2025.108794","DOIUrl":"10.1016/j.biotechadv.2025.108794","url":null,"abstract":"<div><div>Human milk oligosaccharides (HMOs) are complex carbohydrates crucial for infant nutrition, with lacto-N-neotetraose (LNnT) being a key acetylated component that makes up about 10 % of total HMOs. The synthesis of LNnT involves a sequential enzymatic process that modifies lactose, facilitated by β-1,3-<em>N</em>-acetylglucosaminyltransferase (β3GNT) and β-1,4-galactosyltransferase (β4GalT) using UDP-GlcNAc and UDP-Gal as substrates. This review highlights significant advancements in microbial LNnT production, focusing on two main areas: (1) innovations in enzyme engineering that improve glycosyltransferase activity and specificity through computational redesign and directed evolution; (2) strategies for optimizing metabolic flux to balance precursors using modular pathways and transporter controls. Ongoing challenges include enhancing glycosyltransferase specificity to reduce unwanted reactions and managing the complex regulatory networks of precursor flow. New approaches that utilize enzyme design for better catalytic efficiency and adaptive pathway control in response to metabolic changes appear promising for large-scale food additive production. By combining these advancements with GRAS-certified microbial platforms, future bioprocesses can tackle economic challenges while adhering to strict food safety regulations. This overview highlights the need to advance LNnT production from experimental stages to reliable, cost-effective bioprocessing systems that meet the needs of the global food industry.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108794"},"PeriodicalIF":12.5,"publicationDate":"2025-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145877548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-29DOI: 10.1016/j.biotechadv.2025.108786
Juntao Ke, Li Wan, Maiqi Chen, Yizheng Lv, Yingying Zhu, Wenli Zhang, Wanmeng Mu
Spatial engineering has emerged as a transformative paradigm for orchestrating metabolic flux through biomolecular compartmentalization. In cellular systems, the cytosolic dispersion of heterologous enzymes and evolutionary-driven metabolic priorities of native pathways necessitate spatial solutions that transcend conventional enzyme engineering. Concurrently, in vitro metabolons provide critical mechanistic insights into enzymatic cascade reactions through controlled assembly. This review systematically evaluates several spatial engineering platforms for biocatalytic process control—including scaffolded compartments (liposomes, DNA origami, polymersomes, and bacterial microcompartments) and scaffoldless assemblies (membraneless organelles and coacervates)—designed to reconfigure metabolic landscapes in cellular or cell-free contexts. Through critical analysis of recent advances in model construction and functionalized applications, we establish a framework for understanding different spatial control principles governing pathway efficiency and flux redistribution. Finally, we conclude with a comprehensive assessment of current limitations in mechanistic elucidation, dynamic regulation and cross-system compatibility, while projecting future developments towards multifunctional spatial organization tools and biomimetic platforms for synthetic biology and cellular engineering.
{"title":"Spatial engineering for biocatalytic cascade control through biomolecular compartmentalization","authors":"Juntao Ke, Li Wan, Maiqi Chen, Yizheng Lv, Yingying Zhu, Wenli Zhang, Wanmeng Mu","doi":"10.1016/j.biotechadv.2025.108786","DOIUrl":"10.1016/j.biotechadv.2025.108786","url":null,"abstract":"<div><div>Spatial engineering has emerged as a transformative paradigm for orchestrating metabolic flux through biomolecular compartmentalization. In cellular systems, the cytosolic dispersion of heterologous enzymes and evolutionary-driven metabolic priorities of native pathways necessitate spatial solutions that transcend conventional enzyme engineering. Concurrently, in vitro metabolons provide critical mechanistic insights into enzymatic cascade reactions through controlled assembly. This review systematically evaluates several spatial engineering platforms for biocatalytic process control—including scaffolded compartments (liposomes, DNA origami, polymersomes, and bacterial microcompartments) and scaffoldless assemblies (membraneless organelles and coacervates)—designed to reconfigure metabolic landscapes in cellular or cell-free contexts. Through critical analysis of recent advances in model construction and functionalized applications, we establish a framework for understanding different spatial control principles governing pathway efficiency and flux redistribution. Finally, we conclude with a comprehensive assessment of current limitations in mechanistic elucidation, dynamic regulation and cross-system compatibility, while projecting future developments towards multifunctional spatial organization tools and biomimetic platforms for synthetic biology and cellular engineering.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108786"},"PeriodicalIF":12.5,"publicationDate":"2025-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145877516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-27DOI: 10.1016/j.biotechadv.2025.108793
Qinghua Li , Chen Zhang , Jingwen Zhou , Zhaofeng Li , Guocheng Du , Jian Chen , Guoqiang Zhang
Filamentous fungi have emerged as ideal chassis cells for high-value products such as industrial enzymes, therapeutic proteins, and antibiotics, due to their broad substrate adaptability, efficient protein secretion capacity, and well-developed post-translational modification systems. However, the morphological characteristics of filamentous fungi during submerged fermentation present a significant challenge that cannot be overlooked in the biotechnology industry. This review systematically elaborates the fundamental role of polar growth and branching in hyphal morphogenesis and discusses the crucial impact of morphological regulation on fermentation performance. Through in-depth analysis of multi-level strategies, including process-based engineering control, genetic and cell wall modification approaches, and signaling pathway-mediated precise regulation, it clarifies the synergistic mechanisms underlying different regulatory methodologies. The rapid development of technologies such as high-throughput screening, genome editing, multi-omics sequencing, and artificial intelligence has enabled their integration into a collaborative engineering framework through functional complementarity and closed-loop data integration. This system, operating through a workflow of data-driven design, precise editing verification, and intelligent optimization iteration, will significantly enhance the efficiency and precision of morphological regulation. Such technological integration not only provides a systematic theoretical framework and technical guidance for understanding regulatory mechanisms and developing novel strategies, but also promotes the evolution of industrial fermentation toward intelligent and refined processes, thereby offering new technical pathways for green biomanufacturing.
{"title":"Morphological regulation of filamentous fungi improves industrial production","authors":"Qinghua Li , Chen Zhang , Jingwen Zhou , Zhaofeng Li , Guocheng Du , Jian Chen , Guoqiang Zhang","doi":"10.1016/j.biotechadv.2025.108793","DOIUrl":"10.1016/j.biotechadv.2025.108793","url":null,"abstract":"<div><div>Filamentous fungi have emerged as ideal chassis cells for high-value products such as industrial enzymes, therapeutic proteins, and antibiotics, due to their broad substrate adaptability, efficient protein secretion capacity, and well-developed post-translational modification systems. However, the morphological characteristics of filamentous fungi during submerged fermentation present a significant challenge that cannot be overlooked in the biotechnology industry. This review systematically elaborates the fundamental role of polar growth and branching in hyphal morphogenesis and discusses the crucial impact of morphological regulation on fermentation performance. Through in-depth analysis of multi-level strategies, including process-based engineering control, genetic and cell wall modification approaches, and signaling pathway-mediated precise regulation, it clarifies the synergistic mechanisms underlying different regulatory methodologies. The rapid development of technologies such as high-throughput screening, genome editing, multi-omics sequencing, and artificial intelligence has enabled their integration into a collaborative engineering framework through functional complementarity and closed-loop data integration. This system, operating through a workflow of data-driven design, precise editing verification, and intelligent optimization iteration, will significantly enhance the efficiency and precision of morphological regulation. Such technological integration not only provides a systematic theoretical framework and technical guidance for understanding regulatory mechanisms and developing novel strategies, but also promotes the evolution of industrial fermentation toward intelligent and refined processes, thereby offering new technical pathways for green biomanufacturing.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108793"},"PeriodicalIF":12.5,"publicationDate":"2025-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145845088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-27DOI: 10.1016/j.biotechadv.2025.108785
Hang Chen , Ying Shi , Meiling Yuan , Huihui Li , Xiaowei Liu
Target identification is pivotal for developing novel therapeutics in cancer and other diseases. Traditional experiment screening methods are constrained by low throughput and the complexity of biological systems. Multi-omics technologies offer a transformative solution by providing comprehensive, multi-dimensional insights into molecular mechanisms. However, the exponential growth of multi-omics data necessitates efficient computational algorithms for dimensionality reduction and unravel the intricate biological processes. Artificial intelligence (AI) has emerged as a powerful tool capable of analyzing complementary multi-modal data streams. The integration of multi-omics technologies and AI algorithms has revolutionized target identification and drug discovery. This review highlights prevalent omics techniques and their role in target identification and drug discovery, outlines key machine learning (ML) classifications, and describes the integration of multi-omics with AI. We explore the applications of AI-driven multi-omics in various stages of drug discovery, including target identification, target validation, lead optimization, as well as clinical evaluation, underscoring the transformative potential of this approach. Additionally, we discuss the challenges associated with this integrative strategy and future trends in the field. As the integration of multi-omics and AI continues to expand, we anticipate a paradigm shift in target identification and drug discovery, paving the way for more precise and effective therapies.
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Pub Date : 2025-12-26DOI: 10.1016/j.biotechadv.2025.108790
Julián García-Vinuesa , Jorge Rojas , Nicole Soto-García , Nicolás Martínez , Diego Alvarez-Saravia , Roberto Uribe-Paredes , Mehdi D. Davari , Carlos Conca , Juan A. Asenjo , David Medina-Ortiz
Protein engineering is experiencing a paradigmatic transformation through the integration of geometric deep learning (GDL) into computational design workflows. While traditional approaches such as rational design and directed evolution have achieved significant progress, they remain constrained by the vastness of sequence space and the cost of experimental validation. GDL overcomes these limitations by operating on non-Euclidean domains and by capturing the spatial, topological, and physicochemical features that govern protein function.
This perspective provides a comprehensive and critical overview of GDL applications in stability prediction, functional annotation, molecular interaction modeling, and de novo protein design. It consolidates methodological principles, architectural diversity, and performance trends across representative studies, emphasizing how GDL enhances interpretability and generalization in protein science. Aimed at both computational method developers and experimental protein engineers, the review bridges algorithmic concepts with practical design considerations, offering guidance on data representation, model selection, and evaluation strategies.
By integrating explainable artificial intelligence and structure-based validation within a unified conceptual framework, this work highlights how GDL can serve as a foundation for transparent, interpretable, and autonomous protein design. As GDL converges with generative modeling, molecular simulation, and high-throughput experimentation, it is poised to become a cornerstone technology for next-generation protein engineering and synthetic biology.
{"title":"Geometric deep learning assists protein engineering. Opportunities and Challenges","authors":"Julián García-Vinuesa , Jorge Rojas , Nicole Soto-García , Nicolás Martínez , Diego Alvarez-Saravia , Roberto Uribe-Paredes , Mehdi D. Davari , Carlos Conca , Juan A. Asenjo , David Medina-Ortiz","doi":"10.1016/j.biotechadv.2025.108790","DOIUrl":"10.1016/j.biotechadv.2025.108790","url":null,"abstract":"<div><div>Protein engineering is experiencing a paradigmatic transformation through the integration of geometric deep learning (GDL) into computational design workflows. While traditional approaches such as rational design and directed evolution have achieved significant progress, they remain constrained by the vastness of sequence space and the cost of experimental validation. GDL overcomes these limitations by operating on non-Euclidean domains and by capturing the spatial, topological, and physicochemical features that govern protein function.</div><div>This perspective provides a comprehensive and critical overview of GDL applications in stability prediction, functional annotation, molecular interaction modeling, and <em>de novo</em> protein design. It consolidates methodological principles, architectural diversity, and performance trends across representative studies, emphasizing how GDL enhances interpretability and generalization in protein science. Aimed at both computational method developers and experimental protein engineers, the review bridges algorithmic concepts with practical design considerations, offering guidance on data representation, model selection, and evaluation strategies.</div><div>By integrating explainable artificial intelligence and structure-based validation within a unified conceptual framework, this work highlights how GDL can serve as a foundation for transparent, interpretable, and autonomous protein design. As GDL converges with generative modeling, molecular simulation, and high-throughput experimentation, it is poised to become a cornerstone technology for next-generation protein engineering and synthetic biology.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108790"},"PeriodicalIF":12.5,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145845092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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