Pub Date : 2025-10-16DOI: 10.1016/j.biotechadv.2025.108742
Huan Chen , Ya-Ting Gao , Xu-Zhe Ge , Xin Wang , Feng Cheng , Ya-Ping Xue , Yu-Guo Zheng
Material-binding peptides (MBPs) can specifically bind to materials under mild conditions, such as room temperature and aqueous environments, thereby offering promising applications in both biotechnology and materials science. Recent advances in screening techniques, including phage display, bacterial display, and proteomics-based methods, combined with innovations in protein engineering and machine learning, have significantly accelerated the discovery and optimization of MBPs. These peptides have been successfully applied in areas such as catalyst immobilization (biocatalysis), biodegradation, and biomimetic mineralization. This review provides a comprehensive synthesis of the state-of-the-art in MBP research. It begins by discussing the sources of MBPs and the engineering strategies used to enhance their performance, then delves into the molecular mechanisms underlying their material interactions, and finally examines their emerging industrial applications. The review aims to guide researchers through current screening methodologies, provide mechanistic insights, and explore practical applications, offering a roadmap for future advancements in the field.
{"title":"Material-binding peptides: sources, mechanisms, directed evolution and applications","authors":"Huan Chen , Ya-Ting Gao , Xu-Zhe Ge , Xin Wang , Feng Cheng , Ya-Ping Xue , Yu-Guo Zheng","doi":"10.1016/j.biotechadv.2025.108742","DOIUrl":"10.1016/j.biotechadv.2025.108742","url":null,"abstract":"<div><div>Material-binding peptides (MBPs) can specifically bind to materials under mild conditions, such as room temperature and aqueous environments, thereby offering promising applications in both biotechnology and materials science. Recent advances in screening techniques, including phage display, bacterial display, and proteomics-based methods, combined with innovations in protein engineering and machine learning, have significantly accelerated the discovery and optimization of MBPs. These peptides have been successfully applied in areas such as catalyst immobilization (biocatalysis), biodegradation, and biomimetic mineralization. This review provides a comprehensive synthesis of the state-of-the-art in MBP research. It begins by discussing the sources of MBPs and the engineering strategies used to enhance their performance, then delves into the molecular mechanisms underlying their material interactions, and finally examines their emerging industrial applications. The review aims to guide researchers through current screening methodologies, provide mechanistic insights, and explore practical applications, offering a roadmap for future advancements in the field.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108742"},"PeriodicalIF":12.5,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318213","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 : 2025-10-15DOI: 10.1016/j.biotechadv.2025.108738
Galib Khan , Carrie Sanford , Cong T. Trinh
Recombinant protein production (RPP) is central to biotechnology, where recombinant proteins are used as either end products or catalysts in the synthesis of chemicals, fuels, and materials. Among the major cost drivers, culture medium plays a pivotal role in determining protein yield and quality. This review presents a comprehensive perspective on the critical stages of “smart” culture medium optimization: planning, screening, modeling, optimization, and validation. In the planning stage, we examine the nutritional and energetic roles of medium components, including carbon, nitrogen, amino acids, salts, and trace metals, and their impacts on culture parameters such as pH, oxidative state, and osmolality. We highlight the variability in trace metal content due to water sources, culture vessels, and raw materials, which can substantially influence RPP. The screening stage covers Design of Experiments (DoE) approaches, assessing their theoretical basis, implementation, and limitations. For modeling, we describe methods that integrate experimental data to develop predictive models for smart medium formulation. Model-based optimization strategies can then be employed to select optimal media compositions for a given application. The validation stage aims to evaluate model predictions and provide feedback for model training and refinement. Finally, we survey mechanistic and artificial intelligence/machine learning (AI/ML)-driven models as integrated, transformational tools for predictive modeling of bioprocess conditions, nutrient availability, cellular metabolism, and protein quality, with the goal of optimizing culture media to enhance protein yields while reducing costs and environmental impact. We conclude by addressing the challenges of translating laboratory-scale medium optimization to industrial-scale settings and exploring future AI/ML-driven approaches that may overcome current bottlenecks and accelerate medium design for RPP. Overall, this review provides a unified framework for advancing smart medium design in RPP.
{"title":"Smart culture medium optimization for recombinant protein production: Experimental, modeling, and AI/ML-driven strategies","authors":"Galib Khan , Carrie Sanford , Cong T. Trinh","doi":"10.1016/j.biotechadv.2025.108738","DOIUrl":"10.1016/j.biotechadv.2025.108738","url":null,"abstract":"<div><div>Recombinant protein production (RPP) is central to biotechnology, where recombinant proteins are used as either end products or catalysts in the synthesis of chemicals, fuels, and materials. Among the major cost drivers, culture medium plays a pivotal role in determining protein yield and quality. This review presents a comprehensive perspective on the critical stages of “smart” culture medium optimization: planning, screening, modeling, optimization, and validation. In the planning stage, we examine the nutritional and energetic roles of medium components, including carbon, nitrogen, amino acids, salts, and trace metals, and their impacts on culture parameters such as pH, oxidative state, and osmolality. We highlight the variability in trace metal content due to water sources, culture vessels, and raw materials, which can substantially influence RPP. The screening stage covers Design of Experiments (DoE) approaches, assessing their theoretical basis, implementation, and limitations. For modeling, we describe methods that integrate experimental data to develop predictive models for smart medium formulation. Model-based optimization strategies can then be employed to select optimal media compositions for a given application. The validation stage aims to evaluate model predictions and provide feedback for model training and refinement. Finally, we survey mechanistic and artificial intelligence/machine learning (AI/ML)-driven models as integrated, transformational tools for predictive modeling of bioprocess conditions, nutrient availability, cellular metabolism, and protein quality, with the goal of optimizing culture media to enhance protein yields while reducing costs and environmental impact. We conclude by addressing the challenges of translating laboratory-scale medium optimization to industrial-scale settings and exploring future AI/ML-driven approaches that may overcome current bottlenecks and accelerate medium design for RPP. Overall, this review provides a unified framework for advancing smart medium design in RPP.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108738"},"PeriodicalIF":12.5,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145312343","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}
Circular RNAs (circRNAs) have recently garnered significant attention due to their emerging regulatory roles across eukaryotic organisms. These non-coding RNA molecules are generated through a non-canonical back-splicing mechanism that covalently joins the 5′ and 3′ ends, resulting in a closed-loop structure. Although the complete functional landscape of circRNAs remains to be elucidated, advances in RNA sequencing technologies and computational biology have accelerated their identification and functional annotation in both plant and mammalian systems. CircRNAs are increasingly implicated in the regulation of key cellular and metabolic processes, including transcription, translation, protein-protein interactions, cellular proliferation, development, and stress responses, thereby contributing to homeostasis and survival. In this study, we present a comprehensive overview of circRNA biogenesis, structural features, biological roles, and bioinformatic tools used for their prediction in eukaryotes. However, no prior studies have systematically characterized circRNAs in microalgae. To address this gap, we analyzed RNA-seq datasets from three phylogenetically distinct microalgal species (e.g., Chlamydomonas reinhardtii, Dunaliella salina, and Phaeodactylum tricornutum) using the CIRI2 pipeline to identify putative circRNAs. Our analysis revealed candidate circRNAs potentially involved in essential biological pathways, including RNA transcription regulation, mRNA splicing, translational control, chlorophyll function, cytochrome c maintenance, and various post-transcriptional and post-translational modifications. These findings offer novel insights into the regulatory landscape of circRNAs in microalgal species and lay the groundwork for future functional investigations.
{"title":"Circular RNAs in microalgae: Uncovering their biological significance","authors":"Jaber Dehghani , Bahman Panahi , Jens Mortansson Jelstrup Nolsøe , Patrice Lerouge , Muriel Bardor , Yadollah Omidi","doi":"10.1016/j.biotechadv.2025.108739","DOIUrl":"10.1016/j.biotechadv.2025.108739","url":null,"abstract":"<div><div>Circular RNAs (circRNAs) have recently garnered significant attention due to their emerging regulatory roles across eukaryotic organisms. These non-coding RNA molecules are generated through a non-canonical back-splicing mechanism that covalently joins the 5′ and 3′ ends, resulting in a closed-loop structure. Although the complete functional landscape of circRNAs remains to be elucidated, advances in RNA sequencing technologies and computational biology have accelerated their identification and functional annotation in both plant and mammalian systems. CircRNAs are increasingly implicated in the regulation of key cellular and metabolic processes, including transcription, translation, protein-protein interactions, cellular proliferation, development, and stress responses, thereby contributing to homeostasis and survival. In this study, we present a comprehensive overview of circRNA biogenesis, structural features, biological roles, and bioinformatic tools used for their prediction in eukaryotes. However, no prior studies have systematically characterized circRNAs in microalgae. To address this gap, we analyzed RNA-seq datasets from three phylogenetically distinct microalgal species (e.g., <em>Chlamydomonas reinhardtii</em>, <em>Dunaliella salina</em>, and <em>Phaeodactylum tricornutum</em>) using the CIRI2 pipeline to identify putative circRNAs. Our analysis revealed candidate circRNAs potentially involved in essential biological pathways, including RNA transcription regulation, mRNA splicing, translational control, chlorophyll function, cytochrome <em>c</em> maintenance, and various post-transcriptional and post-translational modifications. These findings offer novel insights into the regulatory landscape of circRNAs in microalgal species and lay the groundwork for future functional investigations.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108739"},"PeriodicalIF":12.5,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145312350","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 : 2025-10-14DOI: 10.1016/j.biotechadv.2025.108737
Yu Wang , Yu Tian , Marie Sofie Møller , Zhengyu Jin , Xiaoxiao Li , Birte Svensson
4-α-Glucanotransferases (4αGTs), also known as amylomaltases or disproportionating enzymes, catalyze α-1,4-glucan and maltooligosaccharide transfer in starch and glycogen metabolism of microorganisms, plants and animals. The present review covers their classification, reactions, structure-function relationships, engineering and applications. 4αGTs belong to glycoside hydrolase families GH13, GH57, and GH77, and catalyze four types of reactions: disproportionation, cyclization, coupling, and hydrolysis, of which the first two are particularly important for biotechnological applications. Insights into active site structures and substrate binding have facilitated the rational design of product specificity, modes of action, and increased product yields. Assays of the four reactions encompass monitoring amylose consumption by iodine staining, release of glucose in maltotriose disproportionation, chromatographic analysis of change in chain lengths, and release of reducing sugar by hydrolysis. Major reactions in transglycosylation of starch include formation of amylopectin with extended branch chains and cyclization to large-ring cyclodextrins (LR-CDs), also referred to as cycloamyloses (CAs). Product yields, chain length distribution, and size of LR-CDs depend on the enzyme, substrates and reaction conditions. 4αGT products are useful in the food, biomaterials and pharma sectors. Thus, chain length modification can elicit resistance of starch to digestion via structural reorganization and confer thermo-reversible gel formation, while LR-CDs can increase aqueous solubility of guest-molecules for controlled delivery and adjust rheological behavior of starches. Moreover, 4αGT can generate bioactive glycoconjugates and novel oligosaccharides by transglycosylation. Future development of 4αGT-catalyzed reactions includes optimization by rational enzyme engineering and high-throughput screening technologies. This review portrays the immense potential of 4αGTs in sustainable biomanufacturing.
{"title":"Exploring the enzymatic landscape of 4-α-glucanotransferases in carbohydrate bioprocessing","authors":"Yu Wang , Yu Tian , Marie Sofie Møller , Zhengyu Jin , Xiaoxiao Li , Birte Svensson","doi":"10.1016/j.biotechadv.2025.108737","DOIUrl":"10.1016/j.biotechadv.2025.108737","url":null,"abstract":"<div><div>4-α-Glucanotransferases (4αGTs), also known as amylomaltases or disproportionating enzymes, catalyze α-1,4-glucan and maltooligosaccharide transfer in starch and glycogen metabolism of microorganisms, plants and animals. The present review covers their classification, reactions, structure-function relationships, engineering and applications. 4αGTs belong to glycoside hydrolase families GH13, GH57, and GH77, and catalyze four types of reactions: disproportionation, cyclization, coupling, and hydrolysis, of which the first two are particularly important for biotechnological applications. Insights into active site structures and substrate binding have facilitated the rational design of product specificity, modes of action, and increased product yields. Assays of the four reactions encompass monitoring amylose consumption by iodine staining, release of glucose in maltotriose disproportionation, chromatographic analysis of change in chain lengths, and release of reducing sugar by hydrolysis. Major reactions in transglycosylation of starch include formation of amylopectin with extended branch chains and cyclization to large-ring cyclodextrins (LR-CDs), also referred to as cycloamyloses (CAs). Product yields, chain length distribution, and size of LR-CDs depend on the enzyme, substrates and reaction conditions. 4αGT products are useful in the food, biomaterials and pharma sectors. Thus, chain length modification can elicit resistance of starch to digestion via structural reorganization and confer thermo-reversible gel formation, while LR-CDs can increase aqueous solubility of guest-molecules for controlled delivery and adjust rheological behavior of starches. Moreover, 4αGT can generate bioactive glycoconjugates and novel oligosaccharides by transglycosylation. Future development of 4αGT-catalyzed reactions includes optimization by rational enzyme engineering and high-throughput screening technologies. This review portrays the immense potential of 4αGTs in sustainable biomanufacturing.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108737"},"PeriodicalIF":12.5,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306773","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 : 2025-10-13DOI: 10.1016/j.biotechadv.2025.108736
Nadja Alina Henke , Boas Pucker , Alexander Grünberger
Transcriptomic analyses represent widely used state-of-the art methodologies in molecular biosciences going back to the early 1960s. Over the last years, transcriptomics has become increasingly important in the field of bioprocess engineering. Systematic transcriptomics platform technologies (especially RNA-seq) play an accelerating role to investigate the gene expression profiles of cells in diverse bioprocesses, covering prokaryotic and eukaryotic cell systems. This review summarizes how different transcriptomics methodologies from RT-qPCR to microarrays and RNA-seq have been applied in bioprocess engineering to date. The major scopes of the reviewed works can be categorized as the following: strain/cell line characterization, investigation of culture/media conditions, process operations as well as scale-up/down studies. Subsequently, a perspective is given how emerging sequencing-based transcriptomics could envision the understanding of population diversities in space and time aided by single cell analysis (scRNA-seq) as well as transcriptional histories (Record-Seq).
{"title":"Decoding bioprocesses with transcriptomics: current status and future potential","authors":"Nadja Alina Henke , Boas Pucker , Alexander Grünberger","doi":"10.1016/j.biotechadv.2025.108736","DOIUrl":"10.1016/j.biotechadv.2025.108736","url":null,"abstract":"<div><div>Transcriptomic analyses represent widely used state-of-the art methodologies in molecular biosciences going back to the early 1960s. Over the last years, transcriptomics has become increasingly important in the field of bioprocess engineering. Systematic transcriptomics platform technologies (especially RNA-seq) play an accelerating role to investigate the gene expression profiles of cells in diverse bioprocesses, covering prokaryotic and eukaryotic cell systems. This review summarizes how different transcriptomics methodologies from RT-qPCR to microarrays and RNA-seq have been applied in bioprocess engineering to date. The major scopes of the reviewed works can be categorized as the following: strain/cell line characterization, investigation of culture/media conditions, process operations as well as scale-up/down studies. Subsequently, a perspective is given how emerging sequencing-based transcriptomics could envision the understanding of population diversities in space and time aided by single cell analysis (scRNA-seq) as well as transcriptional histories (Record-Seq).</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108736"},"PeriodicalIF":12.5,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145298396","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 : 2025-10-12DOI: 10.1016/j.biotechadv.2025.108735
Yi Liang, Jiadong Yu , Zonglu Yao, Yuxuan Sun, Jing Feng, Ruixia Shen, Juan Luo, Lixin Zhao
The anaerobic biosynthesis of medium-chain fatty acids (MCFAs) as valorized bio-based chemicals relies on intricate and dynamic interaction networks within microbial communities. This review systematically summarizes the key mechanisms and regulatory strategies driving MCFA biosynthesis in terms of microbial interactions, with a focus on electron donor-acceptor generation and chain elongation (CE) processes. The functional stability and resilience of anaerobic fermentation systems are collectively sustained by microbial diversity via modular functional partitioning, metabolic complementarity, resilience against perturbations, and environmental adaptation. Notably, substrate competition and syntrophic symbiosis between functional taxa directly govern the directionality and efficiency of the metabolic flux. Carbon source preferences and environmental factors synergistically steer pathway selection, while exogenous interventions such as enhanced electron transfer or niche occupation optimize microbial cooperation. In addition, quorum sensing and electrochemical synergy further balance inter-species competition to achieve a dynamic equilibrium between metabolic branch inhibition and enrichment of CE consortia. These multidimensional interaction mechanisms provide high-purity electron donors and stable metabolic foundations for MCFA synthesis to guide directional microbial engineering strategies to enhance product yields. This study systematically summarized how microbial interaction networks drive efficient MCFA biosynthesis via a multi-scale coordination between various mechanisms, including metabolic flux partitioning control, environmental response feedback, and functional modularization design, providing a theoretical foundation for resolving critical challenges during anaerobic MCFA fermentation.
{"title":"Decoding microbial interactions: Interaction networks and regulatory strategies for medium-chain fatty acid biosynthesis through anaerobic chain elongation","authors":"Yi Liang, Jiadong Yu , Zonglu Yao, Yuxuan Sun, Jing Feng, Ruixia Shen, Juan Luo, Lixin Zhao","doi":"10.1016/j.biotechadv.2025.108735","DOIUrl":"10.1016/j.biotechadv.2025.108735","url":null,"abstract":"<div><div>The anaerobic biosynthesis of medium-chain fatty acids (MCFAs) as valorized bio-based chemicals relies on intricate and dynamic interaction networks within microbial communities. This review systematically summarizes the key mechanisms and regulatory strategies driving MCFA biosynthesis in terms of microbial interactions, with a focus on electron donor-acceptor generation and chain elongation (CE) processes. The functional stability and resilience of anaerobic fermentation systems are collectively sustained by microbial diversity via modular functional partitioning, metabolic complementarity, resilience against perturbations, and environmental adaptation. Notably, substrate competition and syntrophic symbiosis between functional taxa directly govern the directionality and efficiency of the metabolic flux. Carbon source preferences and environmental factors synergistically steer pathway selection, while exogenous interventions such as enhanced electron transfer or niche occupation optimize microbial cooperation. In addition, quorum sensing and electrochemical synergy further balance inter-species competition to achieve a dynamic equilibrium between metabolic branch inhibition and enrichment of CE consortia. These multidimensional interaction mechanisms provide high-purity electron donors and stable metabolic foundations for MCFA synthesis to guide directional microbial engineering strategies to enhance product yields. This study systematically summarized how microbial interaction networks drive efficient MCFA biosynthesis via a multi-scale coordination between various mechanisms, including metabolic flux partitioning control, environmental response feedback, and functional modularization design, providing a theoretical foundation for resolving critical challenges during anaerobic MCFA fermentation.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108735"},"PeriodicalIF":12.5,"publicationDate":"2025-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145290854","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 : 2025-10-11DOI: 10.1016/j.biotechadv.2025.108734
Renjie Li, Hanbing Feng, Miao Shi, Aodi Zhang, Su Jing
The burgeoning demand for green manufacturing has spurred significant interest in harnessing biocatalysis across diverse sectors for the synthesis of high value-added compounds. Despite the inherent utility of biocatalysts, their application is often circumscribed by the specificity of the natural enzymes involved. To transcend these limitations, innovative physical and chemical methodologies have been integrated into biocatalytic processes. Physical field interventions, such as the application of mechanical force (force), temperature (heat), light, electricity, and ultrasound (sound) have been employed to engineer reaction systems that facilitate the transformation of substrates into target compounds. On the chemical frontier, metal catalysis, small molecule organocatalysis coupled with biocatalysis in cascade reactions have been revolutionized through several strategies: (I) the one-pot approach, where products are isolated in a stepwise manner by the metal catalysis and biocatalysis; (II) the sequential cascade reaction within a single vessel, wherein enzymes and metal catalysts are introduced simultaneously to amplify product yield; and (III) the cooperative reaction paradigm, where the metal catalyst's product serves as an intermediate or substrate that synergistically interacts with the enzyme to yield the desired product in a one-pot synthesis. This review outlines the research progress in physical and chemical techniques in biocatalysis, aiming to further broaden the reactivity profile of natural enzymes and thereby produce more desired chemicals in past years.
{"title":"Expanding biocatalytic reactivity landscapes by physical fields and chemical strategies for green manufacturing","authors":"Renjie Li, Hanbing Feng, Miao Shi, Aodi Zhang, Su Jing","doi":"10.1016/j.biotechadv.2025.108734","DOIUrl":"10.1016/j.biotechadv.2025.108734","url":null,"abstract":"<div><div>The burgeoning demand for green manufacturing has spurred significant interest in harnessing biocatalysis across diverse sectors for the synthesis of high value-added compounds. Despite the inherent utility of biocatalysts, their application is often circumscribed by the specificity of the natural enzymes involved. To transcend these limitations, innovative physical and chemical methodologies have been integrated into biocatalytic processes. Physical field interventions, such as the application of mechanical force (force), temperature (heat), light, electricity, and ultrasound (sound) have been employed to engineer reaction systems that facilitate the transformation of substrates into target compounds. On the chemical frontier, metal catalysis, small molecule organocatalysis coupled with biocatalysis in cascade reactions have been revolutionized through several strategies: (I) the one-pot approach, where products are isolated in a stepwise manner by the metal catalysis and biocatalysis; (II) the sequential cascade reaction within a single vessel, wherein enzymes and metal catalysts are introduced simultaneously to amplify product yield; and (III) the cooperative reaction paradigm, where the metal catalyst's product serves as an intermediate or substrate that synergistically interacts with the enzyme to yield the desired product in a one-pot synthesis. This review outlines the research progress in physical and chemical techniques in biocatalysis, aiming to further broaden the reactivity profile of natural enzymes and thereby produce more desired chemicals in past years.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108734"},"PeriodicalIF":12.5,"publicationDate":"2025-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145285565","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}
Quorum sensing (QS) is a sophisticated microbial communication system that orchestrates gene expression in response to population density, governing collective behaviors crucial for microbial survival and function. This comprehensive review elucidates the intricate synthesis pathways and mechanisms of QS signaling molecules across diverse microbial species. We critically analyze the multifaceted applications of QS in healthcare, agriculture, and environmental biotechnology, highlighting its potential to revolutionize these fields. The review also explores quorum quenching (QQ) strategies as a novel approach to microbial control and examines the unique adaptations of QS systems in extreme environments. By synthesizing recent advancements and identifying knowledge gaps, we outline pressing challenges and propose promising future research directions. This work aims to provide a roadmap for leveraging QS in developing innovative biotechnological solutions to address global challenges in health, food security, and environmental sustainability.
{"title":"Microbial quorum sensing: Mechanisms, applications, and challenges","authors":"Qi Ruan , Shuting Geng , Jianqiu Yu , Leilei Lu , Yanhua Liu , Jianqiu Chen , Qianjiahua Liao , Ruixin Guo","doi":"10.1016/j.biotechadv.2025.108733","DOIUrl":"10.1016/j.biotechadv.2025.108733","url":null,"abstract":"<div><div>Quorum sensing (QS) is a sophisticated microbial communication system that orchestrates gene expression in response to population density, governing collective behaviors crucial for microbial survival and function. This comprehensive review elucidates the intricate synthesis pathways and mechanisms of QS signaling molecules across diverse microbial species. We critically analyze the multifaceted applications of QS in healthcare, agriculture, and environmental biotechnology, highlighting its potential to revolutionize these fields. The review also explores quorum quenching (QQ) strategies as a novel approach to microbial control and examines the unique adaptations of QS systems in extreme environments. By synthesizing recent advancements and identifying knowledge gaps, we outline pressing challenges and propose promising future research directions. This work aims to provide a roadmap for leveraging QS in developing innovative biotechnological solutions to address global challenges in health, food security, and environmental sustainability.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108733"},"PeriodicalIF":12.5,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249531","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 : 2025-10-03DOI: 10.1016/j.biotechadv.2025.108723
Caroline Rosa Silva , Marcos Pileggi
Water storage tanks contaminated with pesticides serve as a model for an artificial ecosystem in which non-target species, particularly microorganisms, must develop various response mechanisms to survive in such environments. These mechanisms can be classified into non-specific responses, which are associated with various stressors, as well as specific responses to herbicides. Due to the stressful conditions present in these environments, they are regarded as hotspots for the selection of bacterial chassis or consortia of strains that possess combinations of genes encoding diverse phenotypes adapted for survival against a range of toxic substances. This literature review aims to extend the concept of hotspots to other aquatic and terrestrial environments contaminated with pesticides, while also discussing hypotheses regarding the potential exploitation of adapted phenotypes in biotechnological applications. These applications include bioprospecting for microorganisms that produce antimicrobial or antitumor agents, developing live biotherapeutic products for various diseases, and implementing bioremediation strategies. While well established, advances in omics technologies offer new opportunities to enhance the efficiency and safety of these strategies by manipulating gene regulatory systems. However, substantial investment is needed for genetic and metabolic manipulation. Thus, identifying selective hotspots is a beneficial strategy for obtaining viable chassis, as many organisms have already been selected in their ecosystems, along with detailing regulatory systems through omics approaches.
{"title":"Environments contaminated by pesticides are hotspots for the selection of bacterial chassis for biotechnological applications","authors":"Caroline Rosa Silva , Marcos Pileggi","doi":"10.1016/j.biotechadv.2025.108723","DOIUrl":"10.1016/j.biotechadv.2025.108723","url":null,"abstract":"<div><div>Water storage tanks contaminated with pesticides serve as a model for an artificial ecosystem in which non-target species, particularly microorganisms, must develop various response mechanisms to survive in such environments. These mechanisms can be classified into non-specific responses, which are associated with various stressors, as well as specific responses to herbicides. Due to the stressful conditions present in these environments, they are regarded as hotspots for the selection of bacterial chassis or consortia of strains that possess combinations of genes encoding diverse phenotypes adapted for survival against a range of toxic substances. This literature review aims to extend the concept of hotspots to other aquatic and terrestrial environments contaminated with pesticides, while also discussing hypotheses regarding the potential exploitation of adapted phenotypes in biotechnological applications. These applications include bioprospecting for microorganisms that produce antimicrobial or antitumor agents, developing live biotherapeutic products for various diseases, and implementing bioremediation strategies. While well established, advances in omics technologies offer new opportunities to enhance the efficiency and safety of these strategies by manipulating gene regulatory systems. However, substantial investment is needed for genetic and metabolic manipulation. Thus, identifying selective hotspots is a beneficial strategy for obtaining viable chassis, as many organisms have already been selected in their ecosystems, along with detailing regulatory systems through omics approaches.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108723"},"PeriodicalIF":12.5,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145231602","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 : 2025-10-03DOI: 10.1016/j.biotechadv.2025.108722
Yong Chen , Zheng-Dong Qi , Rui Ji , Na Shi , Huayou Chen , Dai-Xu Wei
Polyhydroxyalkanoates (PHAs), characterized by their biodegradability and biocompatibility, present a promising, sustainable alternative to conventional synthetic polymers for biomedical applications. This study highlights the diversity of PHA monomers and structures, controllable biodegradability, and excellent biocompatibility, emphasizing their suitability for tissue engineering (bone, skin, cardiovascular, oral), anti-hair loss treatments, and drug delivery systems. Significant advancements in synthetic biology, encompassing CRISPR/Cas genome editing, promoter engineering, ribosome binding site optimization, metabolic pathway fine-tuning, and morphology engineering, have led to substantial improvements in PHA production efficiency and a reduction in associated costs. The adoption of next-generation industrial biotechnology (NGIB) using halophiles further enhances economic viability and simplifies the production process. The current commercial landscape and the future prospects of medical-grade PHAs, poised to become mainstream biodegradable materials, are also critically discussed.
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