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.
{"title":"Biosensors for coenzyme A thioester derivatives: Development, optimization and applications","authors":"Jing Qiu , Amna Bibi , Alvaro R. Lara , Qinhong Wang , Zongjie Dai","doi":"10.1016/j.biotechadv.2025.108767","DOIUrl":"10.1016/j.biotechadv.2025.108767","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108767"},"PeriodicalIF":12.5,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145619678","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.2025.108772
Nisar Uddin , Muhammad Wajid Ullah , Daochen Zhu , Xiangyang Li , Sanwei Yang , Xin Xie
Lignin biosynthesis and plant cell wall engineering are central to plant structural integrity and biomass utility. Recent advances in molecular and synthetic biology have opened opportunities to tailor lignin contents, composition, and polymer structure for renewable bioenergy and sustainable biomaterial applications. This review provides an integrative perspective on biosynthesis, regulation, and engineering of lignin. It summarizes the current progress in understanding the genetic, transcriptional, epigenetic, and metabolic networks that control lignin formation, with a focus on emerging tools such as CRISPR/Cas genome editing, synthetic promoters, and metabolic rewiring. Beyond cataloguing current knowledge, it critically analyzes the trade-offs involved in lignin modification for biomaterials, addressing unresolved challenges such as monolignol transport, metabolic flux control, and species-specific regulatory divergence. Engineered lignin and modified plant cell walls hold significant potential for biorefineries, advanced polymers, pharmaceuticals, and carbon sequestration, yet their translation from the laboratory to the field remains limited. Engineered lignin offers real-world applications across diverse industries, including bioenergy, bioplastics, carbon fiber composites, pharmaceuticals, and sustainable construction materials, thereby reinforcing its pivotal role in advancing a circular bioeconomy. The review further proposes future research directions that integrate multi-omics, single-cell technologies, machine learning, and field-based validation to enable precision lignin engineering. Strategic advances in this field will support next-generation bioenergy systems, advanced biomaterials, and the transition to a circular bioeconomy.
{"title":"Engineering lignin pathway, plant cell wall modification, and genome editing for advanced renewable bioenergy and material applications","authors":"Nisar Uddin , Muhammad Wajid Ullah , Daochen Zhu , Xiangyang Li , Sanwei Yang , Xin Xie","doi":"10.1016/j.biotechadv.2025.108772","DOIUrl":"10.1016/j.biotechadv.2025.108772","url":null,"abstract":"<div><div>Lignin biosynthesis and plant cell wall engineering are central to plant structural integrity and biomass utility. Recent advances in molecular and synthetic biology have opened opportunities to tailor lignin contents, composition, and polymer structure for renewable bioenergy and sustainable biomaterial applications. This review provides an integrative perspective on biosynthesis, regulation, and engineering of lignin. It summarizes the current progress in understanding the genetic, transcriptional, epigenetic, and metabolic networks that control lignin formation, with a focus on emerging tools such as CRISPR/Cas genome editing, synthetic promoters, and metabolic rewiring. Beyond cataloguing current knowledge, it critically analyzes the trade-offs involved in lignin modification for biomaterials, addressing unresolved challenges such as monolignol transport, metabolic flux control, and species-specific regulatory divergence. Engineered lignin and modified plant cell walls hold significant potential for biorefineries, advanced polymers, pharmaceuticals, and carbon sequestration, yet their translation from the laboratory to the field remains limited. Engineered lignin offers real-world applications across diverse industries, including bioenergy, bioplastics, carbon fiber composites, pharmaceuticals, and sustainable construction materials, thereby reinforcing its pivotal role in advancing a circular bioeconomy. The review further proposes future research directions that integrate multi-omics, single-cell technologies, machine learning, and field-based validation to enable precision lignin engineering. Strategic advances in this field will support next-generation bioenergy systems, advanced biomaterials, and the transition to a circular bioeconomy.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108772"},"PeriodicalIF":12.5,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145619679","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.2025.108771
Yi Zhang , Shulin Deng
Geminiviruses, the largest plant DNA virus family, cause devastating diseases in crops worldwide. These viruses possess distinctive features, such as the stem-loop structure and replication protein (Rep), which enable the creation of functional geminiviral replicons (GVRs) in plants. Over three decades, geminiviruses have been developed into vectors for virus-induced gene silencing (VIGS), high-level protein expression, and genome editing. This review introduces the genomic structure, Rep protein domains and functions, as well as the historical applications of geminiviruses, then highlights their prominent roles in VIGS and synthetic biology. As VIGS vectors, bipartite geminiviruses utilize AV1 gene replacement, while monopartite species rely on satellite DNAs to insert target sequences, enabling gene silencing in diverse plants. In synthetic biology, GVRs facilitate high-level protein expression through autonomous replication and enhance CRISPR/Cas genome editing efficiency in crops. Additionally, gene regulatory elements, including tissue-specific promoters and gene expression enhancement sequences from geminiviral genomes or satellite DNA expand their utility in genetic engineering. Finally, this review provides an outlook on the future development of geminivirus vectors. GVRs can work as plasmid-like DNAs for supporting diverse and creative designs in plant synthetic biology. The stem-loop structure and Rep are not unique to geminiviruses, a fact that suggests potential cross-kingdom applications of GVRs beyond plants. Vast viral resources enable further acceleration of GVR applications through resource mining and optimization. Moreover, attenuated or engineered geminiviral strains hold promise as “plant vaccines” via cross-protection. Collectively, geminivirus vectors bridge fundamental viral research with practical innovations in crop improvement, biomanufacturing, and synthetic biology.
{"title":"Geminivirus vectors: From gene silencing to synthetic biology","authors":"Yi Zhang , Shulin Deng","doi":"10.1016/j.biotechadv.2025.108771","DOIUrl":"10.1016/j.biotechadv.2025.108771","url":null,"abstract":"<div><div>Geminiviruses, the largest plant DNA virus family, cause devastating diseases in crops worldwide. These viruses possess distinctive features, such as the stem-loop structure and replication protein (Rep), which enable the creation of functional geminiviral replicons (GVRs) in plants. Over three decades, geminiviruses have been developed into vectors for virus-induced gene silencing (VIGS), high-level protein expression, and genome editing. This review introduces the genomic structure, Rep protein domains and functions, as well as the historical applications of geminiviruses, then highlights their prominent roles in VIGS and synthetic biology. As VIGS vectors, bipartite geminiviruses utilize <em>AV1</em> gene replacement, while monopartite species rely on satellite DNAs to insert target sequences, enabling gene silencing in diverse plants. In synthetic biology, GVRs facilitate high-level protein expression through autonomous replication and enhance CRISPR/Cas genome editing efficiency in crops. Additionally, gene regulatory elements, including tissue-specific promoters and gene expression enhancement sequences from geminiviral genomes or satellite DNA expand their utility in genetic engineering. Finally, this review provides an outlook on the future development of geminivirus vectors. GVRs can work as plasmid-like DNAs for supporting diverse and creative designs in plant synthetic biology. The stem-loop structure and Rep are not unique to geminiviruses, a fact that suggests potential cross-kingdom applications of GVRs beyond plants. Vast viral resources enable further acceleration of GVR applications through resource mining and optimization. Moreover, attenuated or engineered geminiviral strains hold promise as “plant vaccines” via cross-protection. Collectively, geminivirus vectors bridge fundamental viral research with practical innovations in crop improvement, biomanufacturing, and synthetic biology.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108771"},"PeriodicalIF":12.5,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145619677","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 : 2025-11-28DOI: 10.1016/j.biotechadv.2025.108768
Zhaodong Li , Zihui Gao , Haonan Song , Jialiang He , Wei Xiong
Integrating biological systems with artificial optoelectronic materials for efficient solar energy conversion has emerged as a cutting-edge and promising research direction in the pursuit of sustainable energy solutions. Natural photosynthesis, through intricate biological mechanisms, converts solar energy into chemical energy, serving as an inspiration for human innovation; concurrently, photovoltaic technologies utilize semiconductor materials to directly transform solar radiation into electricity. Recent interdisciplinary research efforts have led to the development of bio-abiotic hybrid interfaces, combining the regenerative capabilities of biological systems with the tunable optoelectronic properties of artificial materials, aiming to enhance solar energy conversion efficiency. This review focuses on the latest advancements in artificial photosynthesis, bio-photoelectrochemical systems, and bio-photovoltaic systems, emphasizing their potential to improve solar energy conversion efficiency. We explore the design principles, operational mechanisms, and performance metrics of these hybrid devices, and conduct an in-depth analysis of technical challenges such as interface stability and electron transfer efficiency. Furthermore, we propose future research directions to optimize these systems for practical applications in sustainable energy production. By integrating knowledge from biology, materials science, and energy engineering, we aim to provide new perspectives and strategies for the development of solar energy conversion technologies, advancing toward more efficient and sustainable energy solutions.
{"title":"Bridging photosynthesis and photovoltaics: Biotechnological pathways for sustainable solar energy","authors":"Zhaodong Li , Zihui Gao , Haonan Song , Jialiang He , Wei Xiong","doi":"10.1016/j.biotechadv.2025.108768","DOIUrl":"10.1016/j.biotechadv.2025.108768","url":null,"abstract":"<div><div>Integrating biological systems with artificial optoelectronic materials for efficient solar energy conversion has emerged as a cutting-edge and promising research direction in the pursuit of sustainable energy solutions. Natural photosynthesis, through intricate biological mechanisms, converts solar energy into chemical energy, serving as an inspiration for human innovation; concurrently, photovoltaic technologies utilize semiconductor materials to directly transform solar radiation into electricity. Recent interdisciplinary research efforts have led to the development of bio-abiotic hybrid interfaces, combining the regenerative capabilities of biological systems with the tunable optoelectronic properties of artificial materials, aiming to enhance solar energy conversion efficiency. This review focuses on the latest advancements in artificial photosynthesis, bio-photoelectrochemical systems, and bio-photovoltaic systems, emphasizing their potential to improve solar energy conversion efficiency. We explore the design principles, operational mechanisms, and performance metrics of these hybrid devices, and conduct an in-depth analysis of technical challenges such as interface stability and electron transfer efficiency. Furthermore, we propose future research directions to optimize these systems for practical applications in sustainable energy production. By integrating knowledge from biology, materials science, and energy engineering, we aim to provide new perspectives and strategies for the development of solar energy conversion technologies, advancing toward more efficient and sustainable energy solutions.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108768"},"PeriodicalIF":12.5,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145611807","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 : 2025-11-27DOI: 10.1016/j.biotechadv.2025.108766
Paul Ahavi , Audrey Le Gouellec , Jean-Loup Faulon
Engineering microbial computers has been a longstanding endeavor in synthetic biology. Like other unconventional computing disciplines, the goal is to bring computation into real-world scenarios. Several potential applications in bioproduction, bioremediation, and biomedicine highlight the promise of this discipline. The first biocomputers were bottom-up predictable circuits that relied on a monoculture-based digital logic and were able to emulate simple logic gates. Drawing from computer theory and extending the analogy with conventional hardware has enabled the engineering of more complex circuits. However, this abstraction soon reached its limits and introduced a semantic gap, which, alongside the constraints imposed by the monoculture paradigm, led to significant scalability limitations such as metabolic burden, orthogonality issues and noisy expression. This review outlines the strategies developed to overcome these issues and engineer more complex biodevices: (i) mitigation strategies that focus on the optimization of the circuits, (ii) multicellular computing that distributes the metabolic load across a consortium and (iii) the implementation of more energy-efficient computing frameworks, such as analog and neuromorphic architectures. While these bottom-up strategies have yielded significant progress, they remain insufficient to emulate the computational complexity of the cellular signal-processing system. In this review, we additionally introduce a new perspective on biocomputing with a top-down approach named reservoir computing. This framework leverages the inherent dynamical computational capabilities and functionalities of biosystems to solve more complex and diverse tasks, thus offering a promising new path for engineering the next generation of microbial computers.
{"title":"Microbial computing: Review and Perspectives","authors":"Paul Ahavi , Audrey Le Gouellec , Jean-Loup Faulon","doi":"10.1016/j.biotechadv.2025.108766","DOIUrl":"10.1016/j.biotechadv.2025.108766","url":null,"abstract":"<div><div>Engineering microbial computers has been a longstanding endeavor in synthetic biology. Like other unconventional computing disciplines, the goal is to bring computation into real-world scenarios. Several potential applications in bioproduction, bioremediation, and biomedicine highlight the promise of this discipline. The first biocomputers were <em>bottom-up</em> predictable circuits that relied on a monoculture-based digital logic and were able to emulate simple logic gates. Drawing from computer theory and extending the analogy with conventional hardware has enabled the engineering of more complex circuits. However, this abstraction soon reached its limits and introduced a semantic gap, which, alongside the constraints imposed by the monoculture paradigm, led to significant scalability limitations such as metabolic burden, orthogonality issues and noisy expression. This review outlines the strategies developed to overcome these issues and engineer more complex biodevices: (i) mitigation strategies that focus on the optimization of the circuits, (ii) multicellular computing that distributes the metabolic load across a consortium and (iii) the implementation of more energy-efficient computing frameworks, such as analog and neuromorphic architectures. While these <em>bottom-up</em> strategies have yielded significant progress, they remain insufficient to emulate the computational complexity of the cellular signal-processing system. In this review, we additionally introduce a new perspective on biocomputing with a <em>top-down</em> approach named reservoir computing. This framework leverages the inherent dynamical computational capabilities and functionalities of biosystems to solve more complex and diverse tasks, thus offering a promising new path for engineering the next generation of microbial computers.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108766"},"PeriodicalIF":12.5,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145609474","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}
The modification of key enzymes for chemical production plays a crucial role in enhancing the yield of targeted products. However, manipulating key nodes in specific signalling pathways remains constrained by traditional gene overexpression or knockout strategies. Discovering and designing optogenetic tools enable us to regulate enzymatic activity or gene expression at key nodes in a spatiotemporal manner, rather than relying solely on chemical induction throughout production processes. In this review, we discuss the recent applications of optogenetic tools in the regulation of microbial metabolites, plant sciences and disease therapies. We categorize optogenetic tools into five classes based on their distinct applications. First, light-induced gene expression schedules can balance the trade-off between chemical production and cell growth phases. Second, light-triggered liquid-liquid phase separation (LLPS) modules provide opportunities to co-localize and condense key enzymes for enhancing catalytic efficiency. Third, light-induced subcellular localized photoreceptors enable the relocation of protein of interest across various subcellular compartments, allowing for the investigation of their dynamic regulatory processes. Fourth, light-regulated enzymes can dynamically regulate production of cyclic nucleotides or investigate endogenous components similar with conditional depletion or recovery function of protein of interest. Fifth, light-gated ion channels and pumps can be utilized to investigate dynamic ion signalling cascades in both animals and plants, or to boost ATP accumulation for enhancing biomass or bioproduct yields in microorganisms. Overall, this review aims to provide a comprehensive overview of optogenetic strategies that have the potential to advance both basic research and bioindustry within the field of synthetic biology.
{"title":"Optogenetic tools for optimizing key signalling nodes in synthetic biology","authors":"Yuehui Tian , Shanshan Xu , Zidong Ye, Huiru Liu, Dongqing Wei, Hossain M. Zabed, Junhua Yun, Guoyan Zhang, Yufei Zhang, Cheng Zhang, Ruiqi Liu, Jia Li, Xianghui Qi","doi":"10.1016/j.biotechadv.2025.108770","DOIUrl":"10.1016/j.biotechadv.2025.108770","url":null,"abstract":"<div><div>The modification of key enzymes for chemical production plays a crucial role in enhancing the yield of targeted products. However, manipulating key nodes in specific signalling pathways remains constrained by traditional gene overexpression or knockout strategies. Discovering and designing optogenetic tools enable us to regulate enzymatic activity or gene expression at key nodes in a spatiotemporal manner, rather than relying solely on chemical induction throughout production processes. In this review, we discuss the recent applications of optogenetic tools in the regulation of microbial metabolites, plant sciences and disease therapies. We categorize optogenetic tools into five classes based on their distinct applications. First, light-induced gene expression schedules can balance the trade-off between chemical production and cell growth phases. Second, light-triggered liquid-liquid phase separation (LLPS) modules provide opportunities to co-localize and condense key enzymes for enhancing catalytic efficiency. Third, light-induced subcellular localized photoreceptors enable the relocation of protein of interest across various subcellular compartments, allowing for the investigation of their dynamic regulatory processes. Fourth, light-regulated enzymes can dynamically regulate production of cyclic nucleotides or investigate endogenous components similar with conditional depletion or recovery function of protein of interest. Fifth, light-gated ion channels and pumps can be utilized to investigate dynamic ion signalling cascades in both animals and plants, or to boost ATP accumulation for enhancing biomass or bioproduct yields in microorganisms. Overall, this review aims to provide a comprehensive overview of optogenetic strategies that have the potential to advance both basic research and bioindustry within the field of synthetic biology.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108770"},"PeriodicalIF":12.5,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145611805","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 : 2025-11-26DOI: 10.1016/j.biotechadv.2025.108769
Ning Liu, Wenfang Liu
By mimicking natural photosynthesis, the photo-enzyme coupling catalysis (PECC) for carbon dioxide conversion integrates the advantages of photocatalysis and enzymatic catalysis, offering an effective and innovative pathway for capture and utilization of greenhouse gas. This review provides a comprehensive overview of recent advancements in this technology, covering the fundamental principles, key components, synergistic mechanisms, compatibility, and future perspectives. A photo-enzyme coupling system (PECS) can be categorized into cofactor-dependent or cofactor-independent system based on the requirement for cofactor mediation. Its main components include photocatalyst and enzyme, which demonstrates unique advantage in the synergism of energy transfer and substrate activation. In order to improve the compatibility of PECS, the strategies including compartmentalized immobilization and process optimization are employed. By developing highly efficient photocatalyst, strengthening interfacial interaction, and optimizing enzyme engineering, PECC holds great promise for transitioning from laboratory research to industrial application, providing robust support for mitigating global climate change and addressing energy crisis.
{"title":"Progress in photo-enzyme coupling catalysis for carbon dioxide reduction","authors":"Ning Liu, Wenfang Liu","doi":"10.1016/j.biotechadv.2025.108769","DOIUrl":"10.1016/j.biotechadv.2025.108769","url":null,"abstract":"<div><div>By mimicking natural photosynthesis, the photo-enzyme coupling catalysis (PECC) for carbon dioxide conversion integrates the advantages of photocatalysis and enzymatic catalysis, offering an effective and innovative pathway for capture and utilization of greenhouse gas. This review provides a comprehensive overview of recent advancements in this technology, covering the fundamental principles, key components, synergistic mechanisms, compatibility, and future perspectives. A photo-enzyme coupling system (PECS) can be categorized into cofactor-dependent or cofactor-independent system based on the requirement for cofactor mediation. Its main components include photocatalyst and enzyme, which demonstrates unique advantage in the synergism of energy transfer and substrate activation. In order to improve the compatibility of PECS, the strategies including compartmentalized immobilization and process optimization are employed. By developing highly efficient photocatalyst, strengthening interfacial interaction, and optimizing enzyme engineering, PECC holds great promise for transitioning from laboratory research to industrial application, providing robust support for mitigating global climate change and addressing energy crisis.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108769"},"PeriodicalIF":12.5,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145609473","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 : 2025-11-21DOI: 10.1016/j.biotechadv.2025.108764
Kumar Vishven Naveen , Akanksha Tyagi , Omnia Mohammed Hamid Ibrahium, Rainer E.A.W. Fischer, Raluca Ostafe
Cell viability assays (CVAs) are widely used in cell biology, biomedical research, drug development, and biotechnology to assess cell health, proliferation, cytotoxicity, and functional activity under various conditions. Key applications span from everyday cell culture monitoring to drug screening and toxicology studies, immunology, vaccine development, and stem cell and regenerative medicine. Despite the long history and widespread use of CVAs, selecting the right assay remains a challenge for researchers. The increasing number of available assay options has led to confusion and inefficiencies, as scientists struggle to navigate the differences, trade-offs, and technical limitations of each method. Many researchers continue using the assays they were trained with, rather than exploring newer, more sensitive, or more appropriate techniques. Lab protocols are often passed down without reassessment, and new projects frequently adopt assays based on convenience (e.g., reagent availability or existing equipment) rather than rational selection criteria. Some groups deliberately choose less sensitive assays under the assumption that they produce “better-distributed” data. However, this incorrect justification arises because assays with a high limit of detection (LOD) fail to capture small variations, creating the misleading perception of clean and well-distributed data. Ignoring small variations does not improve accuracy - it simply reduces sensitivity, potentially leading to incorrect conclusions. Hence, the purpose of this review is to provide a comprehensive overview of contemporary CVAs by categorizing detection methods and summarizing their concepts, applications, benefits, and limitations, while also highlighting the potential need for novel approaches in this field. To assist researchers in selecting the most appropriate assay for their experimental goals, we also present a visual decision tree that integrates mechanistic insights with practical considerations.
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