Biotechnology advances最新文献

{"title":"AI-driven de novo enzyme design: Strategies, applications, and future prospects","authors":"Xi-Chen Cui ,&nbsp;Yan Zheng ,&nbsp;Ye Liu ,&nbsp;Zhiguang Yuchi ,&nbsp;Ying-Jin Yuan","doi":"10.1016/j.biotechadv.2025.108603","DOIUrl":"10.1016/j.biotechadv.2025.108603","url":null,"abstract":"<div><div>Enzymes are indispensable for biological processes and diverse applications across industries. While top-down modification strategies, such as directed evolution, have achieved remarkable success in optimizing existing enzymes, bottom-up <em>de novo</em> enzyme design has emerged as a transformative approach for engineering novel enzymes with customized catalytic functions, independent of natural templates. Recent advancements in artificial intelligence (AI) and computational power have significantly accelerated this field, enabling breakthroughs in enzyme engineering. These technologies facilitate the rapid generation of enzyme structures and amino acid sequences optimized for specific functions, thereby enhancing design efficiency. They also support functional validation and activity optimization, improving the catalytic performance, stability, and robustness of <em>de novo</em> designed enzymes. This review highlights recent advancements in AI-driven <em>de novo</em> enzyme design, discusses strategies for validation and optimization, and examines the challenges and future prospects of integrating these technologies into enzyme development.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"82 ","pages":"Article 108603"},"PeriodicalIF":12.1,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144067199","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}

{"title":"Enzymatic de novo oligonucleotide synthesis: Emerging techniques and advancements","authors":"Nanfeng Gao ,&nbsp;Aimiao Yu ,&nbsp;Weikang Yang ,&nbsp;Xiandi Zhang ,&nbsp;Yue Shen ,&nbsp;Xian Fu","doi":"10.1016/j.biotechadv.2025.108604","DOIUrl":"10.1016/j.biotechadv.2025.108604","url":null,"abstract":"<div><div>Oligonucleotide synthesis serves as a cornerstone of modern life sciences, enabling groundbreaking advancements across molecular diagnostics, therapeutic development, and transformative technologies including DNA data storage and programmable biological systems. While phosphoramidite-based chemical synthesis remains the industrial standard, its limitations in producing long-sequence constructs, cumulative error rates, and reliance on toxic solvents pose significant challenges for next-generation applications. Emerging enzymatic synthesis approaches offer a paradigm shift by harnessing the inherent precision and environmental sustainability of biological systems. This comprehensive review systematically examines the evolving landscape of oligonucleotide synthesis technologies. We first analyze the mechanistic foundations and persistent limitations of conventional chemical methods, followed by a critical evaluation of enzymatic strategies with particular emphasis on terminal deoxynucleotidyl transferase (TdT)-mediated template-independent polymerization. The work provides detailed insights into enzymatic reaction engineering, including substrate specificity profiling of nucleotide analogs and innovative solid-phase synthesis platforms enabling iterative nucleotide addition. Furthermore, we discuss emerging high-throughput synthesis architectures and commercial translation efforts. In summary, this review comprehensively encapsulates the advancements and commercialization status of enzymatic synthesis technologies, offering valuable guidance that can expedite the innovative development of enzymatic oligonucleotide manufacturing platforms.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"82 ","pages":"Article 108604"},"PeriodicalIF":12.1,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075643","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}

{"title":"Recent advances in chemoenzymatic synthesis of human ABO blood group antigens","authors":"Jing Liu ,&nbsp;Xianwei Liu ,&nbsp;Wenyuan Fang","doi":"10.1016/j.biotechadv.2025.108599","DOIUrl":"10.1016/j.biotechadv.2025.108599","url":null,"abstract":"<div><div>ABO blood group antigens (namely, A, B, and H antigens) are carbohydrate epitopes on cell surface that play important roles in biological processes and blood transfusion. The structure diversity of ABH antigens structures is associated with susceptibility to different pathogen infections. Advanced synthetic methodologies are required for studying and applying ABO blood group antigens. The existing methods include chemical, enzymatic and chemoenzymatic synthesis. As an alternative approach to chemical synthesis, enzymatic synthesis provides a simple pathway to access oligosaccharide antigens under extremely mild reaction conditions, thereby avoiding laborious protecting group manipulation procedures. Enzymatic synthesis of human blood group antigens primarily relies on Leloir glycosyltransferases, alongside several glycosidases and glycoside phosphorylases. This review aims to discuss recent advancements in chemical, enzymatic and chemoenzymatic synthesis of human ABH antigens, with a particular focus on novel developments in enzymatic assembly of naturally occurring ABH antigens.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"82 ","pages":"Article 108599"},"PeriodicalIF":12.1,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143947130","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}

{"title":"Sugar phosphatases as biocatalysts for biomanufacturing: Recent advances and applications","authors":"Juanjuan Liu,&nbsp;Guangpeng Xu,&nbsp;Likun Liang,&nbsp;Dongdong Meng","doi":"10.1016/j.biotechadv.2025.108596","DOIUrl":"10.1016/j.biotechadv.2025.108596","url":null,"abstract":"<div><div>Phosphatases, the largest subgroup within the haloacid dehydrogenase (HAD) superfamily, catalyze the irreversible dephosphorylation of phosphate biomolecules. In in vitro synthetic enzymatic biosystems, sugar phosphatases drive the pathways of phosphorylation, transformation (isomerization, epimerization, dehydrogenation, and/or transamination), and dephosphorylation towards product formation through irreversible and exothermic reactions. This process enables enzymatic cascades based on phosphorylation-dephosphorylation to overcome the thermodynamic limitations of traditional functional sugar production methods that rely on isomerases or epimerases, potentially leading to high theoretical conversion rates. However, sugar phosphatases often exhibit broad substrate scope, which can result in dephosphorylation of intermediates within enzymatic biosystems. In this review, we begin by reviewing the classification, structural features, and catalytic mechanisms of phosphatases, followed by the molecular mechanisms underlying substrate promiscuity. The current research on the substrate specificity engineering of phosphatases is then discussed, with particular focus on the production of functional sugars using sugar phosphatase-driven in vitro synthetic enzymatic biosystems. Our goal is to provide a comprehensive overview of the current research status, challenges, and future trends related to sugar phosphatases-mediated biomanufacturing, offers valuable insights into the enzymatic modification and application of these enzymes.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"82 ","pages":"Article 108596"},"PeriodicalIF":12.1,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143967089","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}

{"title":"Polyester-derived monomers as microbial feedstocks: Navigating the landscape of polyester upcycling","authors":"Katerina Foka ,&nbsp;Christina Ferousi ,&nbsp;Evangelos Topakas","doi":"10.1016/j.biotechadv.2025.108589","DOIUrl":"10.1016/j.biotechadv.2025.108589","url":null,"abstract":"<div><div>Since their large-scale adoption in the early 20th century, plastics have become indispensable to modern life. However, inadequate disposal and recycling methods have led to severe environmental consequences. While traditional end-of-life plastics management had predominantly relied on landfilling, a paradigm shift towards recycling and valorization emerged in the 1970s, leading to the development of various, mostly mechanochemical, recycling strategies, together with the more recent approach of biological depolymerization and upcycling. Plastic upcycling, which converts plastic waste into higher-value products, is gaining attention as a sustainable strategy to reduce environmental impact and reliance on virgin materials. Microbial plastic upcycling relies on efficient depolymerization methods to generate monomeric substrates, which are subsequently metabolized by native or engineered microbial systems yielding valuable bioproducts. This review focuses on the second phase of microbial polyester upcycling, examining the intracellular metabolic pathways that enable the assimilation and bioconversion of polyester-derived monomers into industrially relevant compounds. Both biodegradable and non-biodegradable polyesters with commercial significance are considered, with emphasis on pure monomeric feedstocks to elucidate intracellular carbon assimilation pathways. Understanding these metabolic processes provides a foundation for future metabolic engineering efforts, aiming to optimize microbial systems for efficient bioconversion of mixed plastic hydrolysates into valuable bioproducts.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"82 ","pages":"Article 108589"},"PeriodicalIF":12.1,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143947131","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}

{"title":"Enzyme miniaturization: Revolutionizing future biocatalysts","authors":"Ning Ding ,&nbsp;Yaoyukun Jiang ,&nbsp;Sangsin Lee ,&nbsp;Zihao Cheng ,&nbsp;Xinchun Ran ,&nbsp;Yujing Ding ,&nbsp;Robbie Ge ,&nbsp;Yifei Zhang ,&nbsp;Zhongyue J. Yang","doi":"10.1016/j.biotechadv.2025.108598","DOIUrl":"10.1016/j.biotechadv.2025.108598","url":null,"abstract":"<div><div>Enzyme miniaturization offers a transformative approach to overcome limitations posed by the large size of conventional enzymes in industrial, therapeutic, and diagnostic applications. However, the evolutionary optimization of enzymes for activity has not inherently favored compact structures, creating challenges for modern applications requiring smaller catalysts. In this review, we surveyed the advantages of miniature enzymes, including enhanced expressivity, folding efficiency, thermostability, and resistance to proteolysis. We described the applications of miniature enzymes as industrial catalysts, therapeutic agents, and diagnostic elements. We highlighted strategies such as genome mining, rational design, random deletion, and <em>de novo</em> design for achieving enzyme miniaturization, integrating both computational and experimental techniques. By investigating these approaches, we aim to provide a framework for advancing enzyme engineering, emphasizing the unique potential of miniature enzymes to revolutionize biocatalysis, gene therapy, and biosensing technologies.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"82 ","pages":"Article 108598"},"PeriodicalIF":12.1,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143965202","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}

{"title":"Rich analytic toolbox for the exploration, characterization, screening, and application studies of ω-transaminases","authors":"Guan Zhou ,&nbsp;Zewei Zhou ,&nbsp;Dandan Feng ,&nbsp;Wenrui Fan ,&nbsp;Quan Luo ,&nbsp;Xuefeng Lu","doi":"10.1016/j.biotechadv.2025.108597","DOIUrl":"10.1016/j.biotechadv.2025.108597","url":null,"abstract":"<div><div>Omega-transaminases (ωTAs) constitute an important class of biocatalysts in the pharmaceutical, agrochemical, and fine chemical industries, because of their generally good performance in the efficient, enantiospecific, and environment-friendly synthesis of chiral amines that possess diverse chemical structures and biological activities. However, their practical applications are often hindered by unfavorable reaction equilibria, product inhibition, limited robustness, and relatively small accommodation for substrates. Many efforts, including the exploration of novel enzymes from various environments and the targeted engineering of identified enzymes, have been made to develop more specific and efficient ωTA catalysts. A simple, rapid, and accurate evaluation of enzyme activity is important. In addition to the classic chromatography-based methods, to date, at least 18 analytic methods, which are based on cell growth or colorimetry/spectrophotometry, pH, fluorescence and conductivity changes, have been developed and applied in both qualitative and quantitative analyses of ωTAs. These methods differ in terms of their principles, accuracy, throughput, simplicity, and cost-effectiveness. Here, we present a detailed examination of the advantages and drawbacks of these methods. Guidance for method selection from the perspective of practical applications is proposed to assist investigators in choosing appropriate methods according to different research purposes and existing conditions.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"82 ","pages":"Article 108597"},"PeriodicalIF":12.1,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143935781","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}

{"title":"Myxobacteria: Versatile cell factories of novel commercial enzymes for bio-manufacturing","authors":"Zhoukun Li ,&nbsp;Lei Zhang ,&nbsp;Xianfeng Ye ,&nbsp;Yan Huang ,&nbsp;Yanling Ji ,&nbsp;Yuezhong Li ,&nbsp;Daniel Wall ,&nbsp;Zhongli Cui","doi":"10.1016/j.biotechadv.2025.108594","DOIUrl":"10.1016/j.biotechadv.2025.108594","url":null,"abstract":"<div><div>Microbial cell factories for the production of high<strong>-</strong>quality commercial-grade enzymes have accelerated the development of advanced bio-manufacturing approaches, which in turn are environmentally friendly and sustainable. Myxobacteria, a term commonly used to refer to a group within the <em>Myxococcota</em> phylum, are of great interest for their biotechnological applications due to their ability to synthesize a wide range of natural products and lytic enzymes. These traits are essential for the development of robust expression systems. However, myxobacteria have remained an underexploited resource with industrial relevance. Nevertheless, a growing number of food and industrial enzymes have been identified, highlighting myxobacteria as suitable platforms for exploring enzymes with commercial applications, including biomass conversion. Yet, the discovered lytic enzymes are just the tip of the iceberg given their large genomes and diversity across myxobacteria taxa. Despite holding much promise, challenges in genetic engineering, slow growth, and limitations in metabolic remodeling and expression strategies have limited the construction of myxobacterial cell factories. In this review, we highlight recent advances in the discovery of new myxobacterial enzymes and biomass conversion resources, focusing on their potential applications in agriculture and industry. We describe how myxobacteria and their enzymes can be identified through bioprospecting and computational approaches and summarize current biotechnological applications and synthetic biology strategies for bio-manufacturing. Finally, we discuss the promising potential of myxobacteria as industrial cell factories and address open research questions and future directions.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"82 ","pages":"Article 108594"},"PeriodicalIF":12.1,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143924052","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}

{"title":"Technological advancement spurs Komagataella phaffii as a next-generation platform for sustainable biomanufacturing","authors":"Le Gao ,&nbsp;Jie Yuan ,&nbsp;Kai Hong ,&nbsp;Nyuk Ling Ma ,&nbsp;Shuguang Liu ,&nbsp;Xin Wu","doi":"10.1016/j.biotechadv.2025.108593","DOIUrl":"10.1016/j.biotechadv.2025.108593","url":null,"abstract":"<div><div>Biomanufacturing stands as a cornerstone of sustainable industrial development, necessitating a shift toward non-food carbon feedstocks to alleviate agricultural resource competition and advance a circular bioeconomy. Methanol, a renewable one‑carbon substrate, has emerged as a pivotal candidate due to its abundance, cost-effectiveness, and high reduction potential, further bolstered by breakthroughs in CO₂ hydrogenation-based synthesis. Capitalizing on this momentum, the methylotrophic yeast <em>Komagataella phaffii</em> has undergone transformative technological upgrades, evolving from a conventional protein expression workhorse into an intelligent bioproduction chassis. This paradigm shift is fundamentally driven by converging innovations across CRISPR-empowered advancement in genome editing and AI-powered metabolic pathway design in <em>K. phaffii.</em> The integration of CRISPR systems with droplet microfluidics high-throughput screening has redefined strain engineering efficiency, achieving much higher editing precision than traditional homologous recombination while compressing the “design-build-test-learn” cycle. Concurrently, machine learning-enhanced genome-scale metabolic models facilitate dynamic flux balancing, enabling simultaneous improvements in product titers, carbon yields, and volumetric productivity. Finally, technological advancement promotes the application of <em>K. phaffii</em>, including directing more efficiently metabolic flux toward nutrient products, and strengthening efficient synthesis of excreted proteins. As DNA synthesis automation and robotic experimentation platforms mature, next-generation breakthroughs in genome modification, cofactor engineering, and AI-guided autonomous evolution will further cement <em>K. phaffii</em> as a next-generation platform for decarbonizing global manufacturing paradigms. This technological trajectory positions methanol-based biomanufacturing as a cornerstone of the low-carbon circular economy.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"82 ","pages":"Article 108593"},"PeriodicalIF":12.1,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143924050","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}

{"title":"Bacteria-microalgae interactions from an evolutionary perspective and their biotechnological significance","authors":"Ahmad Abd-El-Aziz ,&nbsp;Sherif M. Elnagdy ,&nbsp;Jichang Han ,&nbsp;Rok Mihelič ,&nbsp;Xulei Wang ,&nbsp;Spiros N. Agathos ,&nbsp;Jian Li","doi":"10.1016/j.biotechadv.2025.108591","DOIUrl":"10.1016/j.biotechadv.2025.108591","url":null,"abstract":"<div><div>Interactions between bacteria and microalgae have been studied in natural environments and in industrial consortia. As results of co-evolution for millions of years in nature, they have developed complex symbiotic relationships, including mutualism, commensalism and parasitism, the nature of which is decided by mechanisms of the interaction. There are two main types of molecular interactions between microalgae and bacteria: exchange of nutrients and release of signalling molecules. Nutrient exchange includes transport of organic carbon from microalgae to bacteria and nutrient nitrogen released from nitrogen-fixing bacteria to microalgae, as well as reciprocal supply of micronutrients such as B vitamins and iron. Signalling molecules such as phytohormones secreted by microalgae and quorum sensing molecules secreted by bacteria have been shown to positively affect growth and metabolism of the symbiotic partner. However, there are still a number of potential microalgae-bacteria interactions that have not been well explored, including cyclic peptides, other quorum signalling molecules, and extracellular vesicles involved in exchange of genetic materials. A more thorough understanding of these interactions may not only result in a deeper understanding of the relationships between these symbiotic organisms but also have potential biotechnological applications. Upon new mechanisms of interaction being identified and characterized, novel bioprocesses of synthetic ecology might be developed especially for wastewater treatment and production of biofertilizers and biofuels.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"82 ","pages":"Article 108591"},"PeriodicalIF":12.1,"publicationDate":"2025-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143918022","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}