{"title":"Engineering catalytically promiscuous enzymes to serve new functions.","authors":"Hong-Juan Diao, Li-Ming Lin, Li-Yuan Xu, Jia-Hao Yao, Ren-Chao Zheng, Yu-Guo Zheng","doi":"10.1016/j.biotechadv.2025.108601","DOIUrl":"https://doi.org/10.1016/j.biotechadv.2025.108601","url":null,"abstract":"<p><p>Catalytic promiscuity in enzymes refers to their ability to catalyze multiple chemically distinct reactions in addition to their native activity. The increasing discovery of additional enzymes exhibiting catalytic promiscuity has underscored the significance of this trait in nature. The catalytic promiscuity of enzymes offers new avenues for functional redesign. Through protein engineering, existing enzymes can be modified to expand their natural catalytic boundaries. Furthermore, de novo designed artificial enzymes can achieve novel enzymatic reactions, broadening the scope of enzyme-catalyzed applications. Given that catalytic promiscuity plays a fundamental role in enzyme evolution, comprehensive research on its origins and influencing factors is essential. In this review, we comprehensively examine the factors influencing catalytic promiscuity, including variations in substrate binding modes in pre-reaction states, the instability of key high-energy intermediates, and the roles of critical residues in catalytic mechanisms. Moreover, altering the enzyme's catalytic environment can also induce novel types of catalytic reactions, such as light-induced promiscuous reactions catalyzed by cofactor-dependent oxidoreductase enzymes. Additionally, we summarize the current protein engineering technologies and strategies aimed at enhancing the activity and stereoselectivity of target enzymes to meet industrial requirements.</p>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":" ","pages":"108601"},"PeriodicalIF":12.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075642","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}
Young Sung Jung, Nho-Eul Song, Seo Yeong Oh, Young Kyoung Park, Ye-Jin Kim, Hyunbin Seong, Sang-Mook You, Dong-Hyun Jung, Donghyun Shin, Mi-Gi Lee, Min-Cheol Lim, Nam Soo Han
{"title":"Advances in in vitro cultivation techniques for comprehensive analysis of human gut microbiome.","authors":"Young Sung Jung, Nho-Eul Song, Seo Yeong Oh, Young Kyoung Park, Ye-Jin Kim, Hyunbin Seong, Sang-Mook You, Dong-Hyun Jung, Donghyun Shin, Mi-Gi Lee, Min-Cheol Lim, Nam Soo Han","doi":"10.1016/j.biotechadv.2025.108595","DOIUrl":"https://doi.org/10.1016/j.biotechadv.2025.108595","url":null,"abstract":"<p><p>The role of gut microbiota in human health and disease is becoming increasingly recognized. Historically, the impact of human gut microbiota on health has been studied using clinical trials and animal models. However, clinical studies often struggle with controlling variables and pinpointing disease-causing factors, while animal models fall short of accurately replicating the human gut environment. Additionally, continuous sample collection for gut microbiota analysis in vivo presents significant ethical and technical challenges. To address these limitations, in vitro fermentation models have emerged as promising alternatives. These models aim to simulate the structural and functional characteristics of the human gut in a controlled setting, offering valuable insights into microbial behavior. This review highlights current knowledge and technological advances in in vitro cultivation systems for human gut microbiota, focusing on key elements such as three-dimensional scaffolds, culture media, fermentation systems, and analytical techniques. By examining these components, the review establishes a framework for improving methods to cultivate and study human gut microbiota, enhancing research methodologies for better understanding microbial interactions, behavior, and adaptation in diverse environments.</p>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":" ","pages":"108595"},"PeriodicalIF":12.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075638","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}
Yongmin Zheng , Chen Qi , Yangyi Qiao , Kang Liu , Yanxia Wang , Wankui Jiang , Yujia Jiang , Fengxue Xin , Feng Guo , Wenming Zhang , Min Jiang
{"title":"From formate oxidation to CO₂ reduction: The role of formate dehydrogenase in sustainable carbon utilization","authors":"Yongmin Zheng , Chen Qi , Yangyi Qiao , Kang Liu , Yanxia Wang , Wankui Jiang , Yujia Jiang , Fengxue Xin , Feng Guo , Wenming Zhang , Min Jiang","doi":"10.1016/j.biotechadv.2025.108600","DOIUrl":"10.1016/j.biotechadv.2025.108600","url":null,"abstract":"<div><div>The escalation of global climate change and environmental degradation has made it imperative to develop innovative strategies to mitigate carbon dioxide (CO₂) emissions and enhance its utilization. Formate dehydrogenase (FDH) is a key enzyme capable of catalyzing the reversible conversion between CO₂ and formate. Due to its critical role in sustainable carbon recycling processes, FDH has garnered significant attention in recent times. This review offers a thorough analysis of FDH, emphasizing its dual function of converting one carbon (C1) substrates and providing reducing power. Recent advancements in utilizing FDH for CO₂ reduction, both <em>in vitro</em> and <em>in vivo</em>, underscoring its potential to facilitate carbon capture and conversion under mild conditions. Additionally, this review discusses the limitations of FDH in C1 metabolism and proposes targeted strategies to address these challenges. Future research should focus on achieving a balance between energy production and carbon assimilation, mediated by FDH activity. Ultimately, this work aims to offer both theoretical insights and practical guidance, advancing microbial engineering for CO₂ reduction and resource recycling, and contributing to the development of sustainable carbon utilization technologies.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"82 ","pages":"Article 108600"},"PeriodicalIF":12.1,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143947132","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}
Samantha G. Martinusen , Sage E. Nelson , Ethan W. Slaton , Lawton F. Long , Raymond Pho , Seyednima Ajayebi , Carl A. Denard
{"title":"Protease engineering: Approaches, tools, and emerging trends","authors":"Samantha G. Martinusen , Sage E. Nelson , Ethan W. Slaton , Lawton F. Long , Raymond Pho , Seyednima Ajayebi , Carl A. Denard","doi":"10.1016/j.biotechadv.2025.108602","DOIUrl":"10.1016/j.biotechadv.2025.108602","url":null,"abstract":"<div><div>Engineered proteases with bespoke substrate specificities and activities can empower broad and innovative applications in biomedicine, mass spectrometry-based proteomics, and chemical and synthetic biology. This review provides an authoritative, topical, and detailed description and discussion of the directed evolution and high-throughput strategies designed to engineer the substrate specificity of proteases in <em>E. coli</em>, yeast, phage, and cell-free systems. Second, we discuss emerging protease engineering strategies that complement directed evolution, including antibody-protease fusions that enable proximity catalysis, and protease substrate specificity switching driven by exogenous protein-protein interactions. Lastly, we discuss principles for engineering split and autoinhibited proteases, which are key signal-processing modules in protein circuits. Overall, readers will gain a valuable understanding of the latest advances in protease engineering, focusing on methodologies and strategies that enable precise control of protease activity and specificity.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"82 ","pages":"Article 108602"},"PeriodicalIF":12.1,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144070964","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}
Sebastián Bermúdez-Puga , Bruno Mendes , Jean Pierre Ramos-Galarza , Pamela Oliveira de Souza de Azevedo , Attilio Converti , Francesco Molinari , Simon J. Moore , José R. Almeida , Ricardo Pinheiro de Souza Oliveira
{"title":"Revolutionizing agroindustry: Towards the industrial application of antimicrobial peptides against pathogens and pests","authors":"Sebastián Bermúdez-Puga , Bruno Mendes , Jean Pierre Ramos-Galarza , Pamela Oliveira de Souza de Azevedo , Attilio Converti , Francesco Molinari , Simon J. Moore , José R. Almeida , Ricardo Pinheiro de Souza Oliveira","doi":"10.1016/j.biotechadv.2025.108605","DOIUrl":"10.1016/j.biotechadv.2025.108605","url":null,"abstract":"<div><div>Antibiotics are essential chemicals for medicine and agritech. However, all antibiotics are small molecules that pathogens evolve antimicrobial resistance (AMR). Alternatively, antimicrobial peptides (AMPs) offer potential to overcome or evade AMR. AMPs provide broad-spectrum activity, favourable biosafety profiles, and a rapid and efficient mechanism of action with low resistance incidence. These properties have driven innovative applications, positioning AMPs as promising contributors to advancements in various industrial sectors. This review evaluates the multifaceted nature of AMPs and their biotechnological applications in underexplored sectors. In the food industry, the application of AMPs helps to suppress the growth of microorganisms, thereby decreasing foodborne illnesses, minimizing food waste, and prolonging the shelf life of products. In animal husbandry and aquaculture, incorporating AMPs into the diet reduces the load of pathogenic microorganisms and enhances growth performance and survival rates. In agriculture, AMPs provide an alternative to decrease the use of chemical pesticides and antibiotics. We also review current methods for obtaining AMPs, including chemical synthesis, recombinant DNA technology, cell-free protein synthesis, and molecular farming, are also reviewed. Finally, we look to the peptide market to assess its status, progress, and transition from the discovery stage to benefits for society and high-quality products. Overall, our review exemplifies the other side of the coin of AMPs and how these molecules provide similar benefits to conventional antibiotics and pesticides in the agritech sector.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"82 ","pages":"Article 108605"},"PeriodicalIF":12.1,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144067232","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}
Xi-Chen Cui , Yan Zheng , Ye Liu , Zhiguang Yuchi , Ying-Jin Yuan
{"title":"AI-driven de novo enzyme design: Strategies, applications, and future prospects","authors":"Xi-Chen Cui , Yan Zheng , Ye Liu , Zhiguang Yuchi , 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, Aimiao Yu, Weikang Yang, Xiandi Zhang, Yue Shen, Xian Fu","doi":"10.1016/j.biotechadv.2025.108604","DOIUrl":"https://doi.org/10.1016/j.biotechadv.2025.108604","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":" ","pages":"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 , Xianwei Liu , 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, Guangpeng Xu, Likun Liang, 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}
Katerina Foka , Christina Ferousi , Evangelos Topakas
{"title":"Polyester-derived monomers as microbial feedstocks: Navigating the landscape of polyester upcycling","authors":"Katerina Foka , Christina Ferousi , 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}