Pub Date : 2025-12-18DOI: 10.1016/j.biotechadv.2025.108782
Jiwoo Nam , Yuna Lee , Sion Lee , Hyungjun Choi , Sang Yup Lee , Dongsoo Yang
Microorganisms inhabit diverse environments, including nearly every organ in the human body. The human microbiome—a complex community of microorganisms residing in the human body—has gained increasing attention as a key contributor to human health and disease, making it an important target for the development of diagnostic and therapeutic strategies. However, the inherent complexity of microbial communities and the challenges of engineering diverse non-model microorganisms present significant barriers. To address these challenges, synthetic biology has provided powerful tools and strategies to engineer microorganisms capable of sensing disease-specific environments and performing targeted therapeutic functions. In particular, the development of synthetic genetic circuits has significantly improved the precision and reliability of disease diagnosis and treatment, enabling real-time disease monitoring, therapeutic, and even preventive interventions. This review highlights state-of-the-art synthetic biology tools and strategies for engineering the probiotics and commensal bacteria aimed at the diagnosis and treatment of human diseases, with accompanying examples. Future challenges and prospects are also discussed.
{"title":"Synthetic biology strategies for engineering probiotics and commensal bacteria for diagnostics and therapeutics","authors":"Jiwoo Nam , Yuna Lee , Sion Lee , Hyungjun Choi , Sang Yup Lee , Dongsoo Yang","doi":"10.1016/j.biotechadv.2025.108782","DOIUrl":"10.1016/j.biotechadv.2025.108782","url":null,"abstract":"<div><div>Microorganisms inhabit diverse environments, including nearly every organ in the human body. The human microbiome—a complex community of microorganisms residing in the human body—has gained increasing attention as a key contributor to human health and disease, making it an important target for the development of diagnostic and therapeutic strategies. However, the inherent complexity of microbial communities and the challenges of engineering diverse non-model microorganisms present significant barriers. To address these challenges, synthetic biology has provided powerful tools and strategies to engineer microorganisms capable of sensing disease-specific environments and performing targeted therapeutic functions. In particular, the development of synthetic genetic circuits has significantly improved the precision and reliability of disease diagnosis and treatment, enabling real-time disease monitoring, therapeutic, and even preventive interventions. This review highlights state-of-the-art synthetic biology tools and strategies for engineering the probiotics and commensal bacteria aimed at the diagnosis and treatment of human diseases, with accompanying examples. Future challenges and prospects are also discussed.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108782"},"PeriodicalIF":12.5,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145784803","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 : 2025-12-17DOI: 10.1016/j.biotechadv.2025.108781
Xuan Zhou, Wenyan Cao, Chao Huang, Xiaojuan Zhang, Shenghu Zhou, Yu Deng
Gene expression regulatory elements (GEREs) play a pivotal role in the control of gene transcription and translation. The design of GEREs with precise and tunable activity remains a major challenge in synthetic biology. Over the past decades, engineering strategies have evolved from empirical sequence mining and random mutagenesis to increasingly rational approaches guided by biophysical models and artificial intelligence. In this review, we systematically examine the design principles, representative studies, and implementation strategies for each GERE class, highlighting how mining, modular recombination, targeted mutagenesis, and deep generative modeling contribute to the development of functional regulatory elements. We further discuss the strengths and limitations of these strategies, offering practical guidance for optimizing microbial cell factory bioproduction through the fine-tuning of gene expression.
{"title":"Designing prokaryotic gene expression regulatory elements: From genomic mining to artificial intelligence-driven generation","authors":"Xuan Zhou, Wenyan Cao, Chao Huang, Xiaojuan Zhang, Shenghu Zhou, Yu Deng","doi":"10.1016/j.biotechadv.2025.108781","DOIUrl":"10.1016/j.biotechadv.2025.108781","url":null,"abstract":"<div><div>Gene expression regulatory elements (GEREs) play a pivotal role in the control of gene transcription and translation. The design of GEREs with precise and tunable activity remains a major challenge in synthetic biology. Over the past decades, engineering strategies have evolved from empirical sequence mining and random mutagenesis to increasingly rational approaches guided by biophysical models and artificial intelligence. In this review, we systematically examine the design principles, representative studies, and implementation strategies for each GERE class, highlighting how mining, modular recombination, targeted mutagenesis, and deep generative modeling contribute to the development of functional regulatory elements. We further discuss the strengths and limitations of these strategies, offering practical guidance for optimizing microbial cell factory bioproduction through the fine-tuning of gene expression.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108781"},"PeriodicalIF":12.5,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145784804","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}
Flavin reductases (FRs) are essential redox enzymes that supply reduced flavin cofactors (FMNH−/FADH−) to various monooxygenase partners in two-component flavin-dependent monooxygenase (TC-FDMO) systems. These enzymes play critical roles in numerous biological processes and industrial biocatalytic reactions, including hydroxylation, halogenation, and epoxidation. In this review, we provide a comprehensive analysis of the structural features, oligomeric states, kinetic mechanisms, and newly proposed classification strategies of FRs. We highlight the limitations of existing classification systems that rely solely on physiological function and propose a more informative framework based on amino acid sequences and domain architectures. Detailed mechanistic insights from transient kinetics, charge-transfer complex formation, and flavin transfer pathways are discussed, with emphasis on enzyme-specific features such as half-site reactivity and substrate-enhanced catalysis. Advances in protein engineering and fusion protein design aimed at improving FR stability, catalytic performance, and cofactor regeneration are also critically evaluated. In addition, we explore alternative strategies for supplying reduced flavin to monooxygenase partners, including non-enzymatic regeneration methods and the use of nicotinamide analogs. Finally, we outline key challenges and future directions for developing next-generation FRs with enhanced industrial applicability. This knowledge provides a foundation for engineering TC-FDMO systems for scalable, sustainable, and industrially relevant biocatalysis.
{"title":"Flavin reductases in two-component systems: Mechanistic insights, structural classification, and biotechnological advances","authors":"Panu Pimviriyakul , Piyanuch Anuwan , Pimchai Chaiyen , Thanyaporn Wongnate","doi":"10.1016/j.biotechadv.2025.108779","DOIUrl":"10.1016/j.biotechadv.2025.108779","url":null,"abstract":"<div><div>Flavin reductases (FRs) are essential redox enzymes that supply reduced flavin cofactors (FMNH<sup>−</sup>/FADH<sup>−</sup>) to various monooxygenase partners in two-component flavin-dependent monooxygenase (TC-FDMO) systems. These enzymes play critical roles in numerous biological processes and industrial biocatalytic reactions, including hydroxylation, halogenation, and epoxidation. In this review, we provide a comprehensive analysis of the structural features, oligomeric states, kinetic mechanisms, and newly proposed classification strategies of FRs. We highlight the limitations of existing classification systems that rely solely on physiological function and propose a more informative framework based on amino acid sequences and domain architectures. Detailed mechanistic insights from transient kinetics, charge-transfer complex formation, and flavin transfer pathways are discussed, with emphasis on enzyme-specific features such as half-site reactivity and substrate-enhanced catalysis. Advances in protein engineering and fusion protein design aimed at improving FR stability, catalytic performance, and cofactor regeneration are also critically evaluated. In addition, we explore alternative strategies for supplying reduced flavin to monooxygenase partners, including non-enzymatic regeneration methods and the use of nicotinamide analogs. Finally, we outline key challenges and future directions for developing next-generation FRs with enhanced industrial applicability. This knowledge provides a foundation for engineering TC-FDMO systems for scalable, sustainable, and industrially relevant biocatalysis.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108779"},"PeriodicalIF":12.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145780161","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 : 2025-12-14DOI: 10.1016/j.biotechadv.2025.108780
Jie Wu , Tianjie Ao , Yufeng Yuan , Zhangmin Wan , Richard Chandra , Jack Saddler
Although cellulose can be found in nature in an unassociated form (e.g., cotton, microbially derived cellulose, etc.), it is typically associated with other polymers such as lignin and hemicellulose. However, even “pure” cellulose has proven difficult to hydrolyze, primarily due to the lack of enzyme accessibility to the glycan chains. Thus, typically, much higher protein/enzyme concentrations and longer incubation times are needed as compared to hydrolyzing starch, a related glucose polymer. The “crystalline” structure of most of the cellulose and its close association with other lignocellulosic components (e.g., lignin, etc.) restrict the enzyme accessibility of the cellulase enzyme “cocktail”. Consequently, some form of pretreatment plus the addition of accessory enzymes are typically needed to enhance cellulose hydrolysis. Although biomass-derived sugars can be readily detected and quantified, assessing cellulose accessibility by methods such as pore-volume, Simon's stain, cellulose binding domain (CBM) adsorption, etc., has proven problematic. Effective pretreatment, which maximizes the recovery of biomass components and increases cellulose accessibility, is typically required to achieve high glucose yields from biomass feedstocks. In addition, an optimized “cellulase cocktail,” which further improves accessibility and is more resistant to factors such as end-product inhibition, is usually necessary to reach efficient hydrolysis. The influence of these and other issues are discussed below.
{"title":"The key role that cellulose accessibility plays in restricting enzyme-mediated hydrolysis of cellulose","authors":"Jie Wu , Tianjie Ao , Yufeng Yuan , Zhangmin Wan , Richard Chandra , Jack Saddler","doi":"10.1016/j.biotechadv.2025.108780","DOIUrl":"10.1016/j.biotechadv.2025.108780","url":null,"abstract":"<div><div>Although cellulose can be found in nature in an unassociated form (e.g., cotton, microbially derived cellulose, etc.), it is typically associated with other polymers such as lignin and hemicellulose. However, even “pure” cellulose has proven difficult to hydrolyze, primarily due to the lack of enzyme accessibility to the glycan chains. Thus, typically, much higher protein/enzyme concentrations and longer incubation times are needed as compared to hydrolyzing starch, a related glucose polymer. The “crystalline” structure of most of the cellulose and its close association with other lignocellulosic components (e.g., lignin, etc.) restrict the enzyme accessibility of the cellulase enzyme “cocktail”. Consequently, some form of pretreatment plus the addition of accessory enzymes are typically needed to enhance cellulose hydrolysis. Although biomass-derived sugars can be readily detected and quantified, assessing cellulose accessibility by methods such as pore-volume, Simon's stain, cellulose binding domain (CBM) adsorption, etc., has proven problematic. Effective pretreatment, which maximizes the recovery of biomass components and increases cellulose accessibility, is typically required to achieve high glucose yields from biomass feedstocks. In addition, an optimized “cellulase cocktail,” which further improves accessibility and is more resistant to factors such as end-product inhibition, is usually necessary to reach efficient hydrolysis. The influence of these and other issues are discussed below.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108780"},"PeriodicalIF":12.5,"publicationDate":"2025-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145753507","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 : 2025-12-12DOI: 10.1016/j.biotechadv.2025.108778
Kamila Koppova, Barbora Branska
Lignocellulose represents a sustainable feedstock for the production of platform chemicals, yet its potential is influenced by inhibitory compounds that impair microbial performance. Among microbial producers, solventogenic Clostridium species are particularly promising for bio-based solvent production, notably butanol, but their physiology and productivity are highly sensitive to lignocellulose-derived inhibitors. This review comprehensively summarizes how these inhibitors affect growth, viability, sporulation, membrane integrity, efflux, stress responses, and metabolic pathways, including central metabolism, redox balance, and detoxification, specifically in solventogenic Clostridium species, predominantly Clostridium acetobutylicum, Clostridium beijerinckii, Clostridium saccharobutylicum and Clostridium saccharoperbutylacetonicum. Available studies indicate that cellular responses are complex and depend on both strain and experimental conditions. Knowledge gaps persist regarding the stimulatory effects of certain inhibitors at low concentrations and detoxification pathways involved. To expand information about inhibitor transformation, Clostridium tyrobutyricum, a closely related species, is also included. In addition, strategies for mitigating the negative effects of inhibitors, extending beyond genetic engineering approaches, are discussed. By summarizing the available data, this review aims to support the utilization of solventogenic clostridia as promising producers of solvents and to contribute to their integration into lignocellulose-based industrial biotechnological processes.
{"title":"Physiological response of solventogenic clostridia to lignocellulose-derived inhibitors","authors":"Kamila Koppova, Barbora Branska","doi":"10.1016/j.biotechadv.2025.108778","DOIUrl":"10.1016/j.biotechadv.2025.108778","url":null,"abstract":"<div><div>Lignocellulose represents a sustainable feedstock for the production of platform chemicals, yet its potential is influenced by inhibitory compounds that impair microbial performance. Among microbial producers, solventogenic <em>Clostridium</em> species are particularly promising for bio-based solvent production, notably butanol, but their physiology and productivity are highly sensitive to lignocellulose-derived inhibitors. This review comprehensively summarizes how these inhibitors affect growth, viability, sporulation, membrane integrity, efflux, stress responses, and metabolic pathways, including central metabolism, redox balance, and detoxification, specifically in solventogenic <em>Clostridium</em> species, predominantly <em>Clostridium acetobutylicum</em>, <em>Clostridium beijerinckii, Clostridium saccharobutylicum</em> and <em>Clostridium saccharoperbutylacetonicum</em>. Available studies indicate that cellular responses are complex and depend on both strain and experimental conditions. Knowledge gaps persist regarding the stimulatory effects of certain inhibitors at low concentrations and detoxification pathways involved. To expand information about inhibitor transformation, <em>Clostridium tyrobutyricum</em>, a closely related species, is also included. In addition, strategies for mitigating the negative effects of inhibitors, extending beyond genetic engineering approaches, are discussed. By summarizing the available data, this review aims to support the utilization of solventogenic clostridia as promising producers of solvents and to contribute to their integration into lignocellulose-based industrial biotechnological processes.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108778"},"PeriodicalIF":12.5,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145731097","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 : 2025-12-09DOI: 10.1016/j.biotechadv.2025.108777
Shuman Song , Jiaran Lu , Xiangyun Jiang , Jiaqi Zhao , Xinran Xiang , Yuting Shang
Single-cell analysis affords a novel perspective for deciphering the intricacies of complex biological systems by elucidating the subtle heterogeneities within cellular populations, with particular relevance to cellular development, pathophysiological mechanisms, and therapeutic responsiveness. At present, numerous studies have reported the application of droplet microfluidics in facilitating high-throughput experimentation at the single-cell level through the precise manipulation of individual cells. However, few comprehensive and systematic reviews have focused on the optimization of droplet microfluidic manipulation strategies and the innovative applications of this technology across various fields. This review discusses the ingenious designs for enhancing cell analysis and highlights their applications in the realms of bioassay, immunotherapy, and drug screening. Furthermore, this review summarizes the current research findings on droplet microfluidics and outlines their future development directions.
{"title":"Droplet microfluidics for single-cell analysis: From improved cell encapsulation and sorting technologies to innovative applications","authors":"Shuman Song , Jiaran Lu , Xiangyun Jiang , Jiaqi Zhao , Xinran Xiang , Yuting Shang","doi":"10.1016/j.biotechadv.2025.108777","DOIUrl":"10.1016/j.biotechadv.2025.108777","url":null,"abstract":"<div><div>Single-cell analysis affords a novel perspective for deciphering the intricacies of complex biological systems by elucidating the subtle heterogeneities within cellular populations, with particular relevance to cellular development, pathophysiological mechanisms, and therapeutic responsiveness. At present, numerous studies have reported the application of droplet microfluidics in facilitating high-throughput experimentation at the single-cell level through the precise manipulation of individual cells. However, few comprehensive and systematic reviews have focused on the optimization of droplet microfluidic manipulation strategies and the innovative applications of this technology across various fields. This review discusses the ingenious designs for enhancing cell analysis and highlights their applications in the realms of bioassay, immunotherapy, and drug screening. Furthermore, this review summarizes the current research findings on droplet microfluidics and outlines their future development directions.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108777"},"PeriodicalIF":12.5,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145731760","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 : 2025-12-06DOI: 10.1016/j.biotechadv.2025.108775
Andrea M. Garza Elizondo , Ilenne del Valle Kessra , Erica Teixeira Prates , Evan Komp , Elise K. Phillips , Nandhini Ashok , Daniel A. Jacobson , Erin G. Webb , Yannick J. Bomble , William G. Alexander , Joanna Tannous , Chung-Jui Tsai , Wayne A. Parrott , Xiaohan Yang , Breeanna R. Urbanowicz , Laura E. Bartley , Costas D. Maranas , Gerald A. Tuskan , Adam M. Guss , Carrie A. Eckert
The field of synthetic biology is essential to the continued development of a bio-based economy, creating mechanisms to supply carbon needed in the economy by both converting existing end-of-life wastes as well as by creating novel, purpose-grown and sustainable feedstocks. Here, we first discuss the near- and long-term resources available for use as feedstocks for bioconversion as well as the output molecules needed for building the foundation of an expanded bio-based economy. We then outline the organisms and phenotypic traits that are needed for the performance-advantaged chassis organisms of the future. Furthermore, we detail the advances, challenges, and opportunities in both microbial and plant synthetic biology relevant to expanding the bio-based economy. Finally, we explore technologies that have and will further enable advances in synthetic biology and the greater bio-based economy.
{"title":"Building an expanded bio-based economy through synthetic biology","authors":"Andrea M. Garza Elizondo , Ilenne del Valle Kessra , Erica Teixeira Prates , Evan Komp , Elise K. Phillips , Nandhini Ashok , Daniel A. Jacobson , Erin G. Webb , Yannick J. Bomble , William G. Alexander , Joanna Tannous , Chung-Jui Tsai , Wayne A. Parrott , Xiaohan Yang , Breeanna R. Urbanowicz , Laura E. Bartley , Costas D. Maranas , Gerald A. Tuskan , Adam M. Guss , Carrie A. Eckert","doi":"10.1016/j.biotechadv.2025.108775","DOIUrl":"10.1016/j.biotechadv.2025.108775","url":null,"abstract":"<div><div>The field of synthetic biology is essential to the continued development of a bio-based economy, creating mechanisms to supply carbon needed in the economy by both converting existing end-of-life wastes as well as by creating novel, purpose-grown and sustainable feedstocks. Here, we first discuss the near- and long-term resources available for use as feedstocks for bioconversion as well as the output molecules needed for building the foundation of an expanded bio-based economy. We then outline the organisms and phenotypic traits that are needed for the performance-advantaged chassis organisms of the future. Furthermore, we detail the advances, challenges, and opportunities in both microbial and plant synthetic biology relevant to expanding the bio-based economy. Finally, we explore technologies that have and will further enable advances in synthetic biology and the greater bio-based economy.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108775"},"PeriodicalIF":12.5,"publicationDate":"2025-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145689942","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 : 2025-12-06DOI: 10.1016/j.biotechadv.2025.108776
Jiayun Fu , Xiaoqian Tang , Du Wang , Qi Zhang , Jinsheng Duan , Peiwu Li
Nanobodies (Nbs), the single-domain antigen-binding fragments, have emerged as promising biorecognition elements for immunoassays due to their small size, high stability, strong affinity, and ease of engineering. This review comprehensively summarizes recent advances in Nb-based immunoassay technologies, highlighting their advantages in immunoassay such as phage-displayed Nbs, Nb-reporter fusions, toxin-free substitutes using anti-idiotypic Nbs, reusable immunoaffinity ligands, bispecific Nbs for multi-target detection, and multivalent Nbs to enhance binding avidity. The review further discusses their applications in food safety, clinical diagnostics, and environmental monitoring, highlighting their impact across these fields. Key challenges such as the limited number of available Nbs, low expression levels, and commercialization bottlenecks are discussed, along with emerging solutions like synthetic libraries and computer-aided design. This review aims to provide insights into the development trends and application potential of Nb-based immunoassays, promoting their future advancement in analytical and diagnostic.
{"title":"Advancements of immunoassay technology based on nanobodies","authors":"Jiayun Fu , Xiaoqian Tang , Du Wang , Qi Zhang , Jinsheng Duan , Peiwu Li","doi":"10.1016/j.biotechadv.2025.108776","DOIUrl":"10.1016/j.biotechadv.2025.108776","url":null,"abstract":"<div><div>Nanobodies (Nbs), the single-domain antigen-binding fragments, have emerged as promising biorecognition elements for immunoassays due to their small size, high stability, strong affinity, and ease of engineering. This review comprehensively summarizes recent advances in Nb-based immunoassay technologies, highlighting their advantages in immunoassay such as phage-displayed Nbs, Nb-reporter fusions, toxin-free substitutes using anti-idiotypic Nbs, reusable immunoaffinity ligands, bispecific Nbs for multi-target detection, and multivalent Nbs to enhance binding avidity. The review further discusses their applications in food safety, clinical diagnostics, and environmental monitoring, highlighting their impact across these fields. Key challenges such as the limited number of available Nbs, low expression levels, and commercialization bottlenecks are discussed, along with emerging solutions like synthetic libraries and computer-aided design. This review aims to provide insights into the development trends and application potential of Nb-based immunoassays, promoting their future advancement in analytical and diagnostic.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108776"},"PeriodicalIF":12.5,"publicationDate":"2025-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145689943","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 : 2025-12-02DOI: 10.1016/j.biotechadv.2025.108773
Faheem Tariq , Linmao Zhao , Saddam Hussain , Muhammad Waheed Riaz , Chenglai Wu , Jiwang Zhang , Pinghua Li , Manje Gowda , Sudha K. Nair , Boddupalli M. Prasanna , Xuecai Zhang , Xianglan Wang , Sunil S. Gangurde
Soil salinization poses a major challenge to global food security, affecting over one billion hectares of arable land and severely constraining crop productivity. As the primary interface between plants and soil, roots play a pivotal role in sensing and adapting to salinity stress through remarkable structural and functional plasticity. This review integrates recent advances in root system architecture (RSA) dynamics, suberin biosynthesis, hormonal regulation, and microbiome interactions to elucidate how plants achieve salinity resilience. We discuss key genes and regulatory modules controlling primary root elongation, lateral root patterning, and barrier formation, emphasizing transcriptional networks involving MYB, NAC, and WRKY families and their coordination with ABA, auxin, and ethylene signaling. Special attention is given to the biosynthesis and deposition of suberin as a dynamic ion-selective barrier governed by hormonal crosstalk and lipid metabolism. We further highlight how beneficial microbes such as Azospirillum, Bacillus, and arbuscular mycorrhizal fungi enhance salt tolerance by modulating phytohormones, antioxidant systems, and ionic homeostasis. Integrating multi-omics and CRISPR-based tools with microbiome engineering offers new avenues to design salt-resilient root ideotypes. We propose a conceptual framework linking molecular regulation, hormonal dynamics, and rhizosphere ecology to root system plasticity, providing a blueprint for engineering next-generation crops capable of maintaining growth and productivity in saline environments.
{"title":"Plasticity and adaptive architecture of roots for enhanced salinity tolerance in crops","authors":"Faheem Tariq , Linmao Zhao , Saddam Hussain , Muhammad Waheed Riaz , Chenglai Wu , Jiwang Zhang , Pinghua Li , Manje Gowda , Sudha K. Nair , Boddupalli M. Prasanna , Xuecai Zhang , Xianglan Wang , Sunil S. Gangurde","doi":"10.1016/j.biotechadv.2025.108773","DOIUrl":"10.1016/j.biotechadv.2025.108773","url":null,"abstract":"<div><div>Soil salinization poses a major challenge to global food security, affecting over one billion hectares of arable land and severely constraining crop productivity. As the primary interface between plants and soil, roots play a pivotal role in sensing and adapting to salinity stress through remarkable structural and functional plasticity. This review integrates recent advances in root system architecture (RSA) dynamics, suberin biosynthesis, hormonal regulation, and microbiome interactions to elucidate how plants achieve salinity resilience. We discuss key genes and regulatory modules controlling primary root elongation, lateral root patterning, and barrier formation, emphasizing transcriptional networks involving <em>MYB</em>, <em>NAC</em>, and <em>WRKY</em> families and their coordination with ABA, auxin, and ethylene signaling. Special attention is given to the biosynthesis and deposition of suberin as a dynamic ion-selective barrier governed by hormonal crosstalk and lipid metabolism. We further highlight how beneficial microbes such as <em>Azospirillum</em>, <em>Bacillus</em>, and arbuscular mycorrhizal fungi enhance salt tolerance by modulating phytohormones, antioxidant systems, and ionic homeostasis. Integrating multi-omics and CRISPR-based tools with microbiome engineering offers new avenues to design salt-resilient root ideotypes. We propose a conceptual framework linking molecular regulation, hormonal dynamics, and rhizosphere ecology to root system plasticity, providing a blueprint for engineering next-generation crops capable of maintaining growth and productivity in saline environments.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108773"},"PeriodicalIF":12.5,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145657155","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 : 2025-11-29DOI: 10.1016/j.biotechadv.2025.108767
Jing Qiu , Amna Bibi , Alvaro R. Lara , Qinhong Wang , Zongjie Dai
Coenzyme A thioester derivatives, particularly acetyl-CoA, malonyl-CoA and fatty acyl-CoA, are essential central metabolites in microorganisms. These compounds play pivotal roles in numerous metabolic pathways and serve as key precursors in the biosynthesis of various high-value compounds, including fatty acids, polyketides, and flavonoids. The spatiotemporal distribution of CoA thioester derivatives is variable and tightly regulated, making real-time monitoring worthwhile. Biosensors have emerged as valuable tools for rapid and immediate detection because of their respond to changes of inducers. This has facilitated the development of efficient metabolic engineering strategies, including dynamic regulation and high-throughput screening. In this context, the review offers a comprehensive overview of the current progress, optimization, applications and limitations of biosensors for acetyl-CoA, malonyl-CoA, fatty acyl-CoA and other CoA thioester derivatives. Based on these limitations, it also outlines prospects for further development and discusses potential biosensor elements for CoA thioester derivatives.
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