Pub Date : 2024-12-16DOI: 10.1016/j.biotechadv.2024.108505
Ana C. Afonso , Maria J. Saavedra , Manuel Simões , Lúcia C. Simões
Bacterial coaggregation is a critical process in multispecies biofilm formation, driven by specific molecular interactions that facilitate the adhesion and aggregation of bacterial cells. These interactions are essential for the development and persistence of complex microbial communities. This review provides a comprehensive analysis of the roles of the proteosurfaceome and exoproteome in bacterial coaggregation. The proteosurfaceome, comprising surface-bound molecules such as adhesins, drives species-specific interactions crucial for partner recognition and adhesion. In parallel, the exoproteome, particularly extracellular polymeric substances (EPS), enhances aggregate stability by reinforcing structural integrity and facilitating intercellular communication, although its direct role in coaggregation remains to be fully clarified. By integrating these perspectives, this review aims to elucidate how the proteosurfaceome and exoproteome influence bacterial coaggregation, offering insights into their combined impact on microbial community structure and function. Furthermore, we highlight existing knowledge gaps and propose directions for future research.
{"title":"The role of the proteosurfaceome and exoproteome in bacterial coaggregation","authors":"Ana C. Afonso , Maria J. Saavedra , Manuel Simões , Lúcia C. Simões","doi":"10.1016/j.biotechadv.2024.108505","DOIUrl":"10.1016/j.biotechadv.2024.108505","url":null,"abstract":"<div><div>Bacterial coaggregation is a critical process in multispecies biofilm formation, driven by specific molecular interactions that facilitate the adhesion and aggregation of bacterial cells. These interactions are essential for the development and persistence of complex microbial communities. This review provides a comprehensive analysis of the roles of the proteosurfaceome and exoproteome in bacterial coaggregation. The proteosurfaceome, comprising surface-bound molecules such as adhesins, drives species-specific interactions crucial for partner recognition and adhesion. In parallel, the exoproteome, particularly extracellular polymeric substances (EPS), enhances aggregate stability by reinforcing structural integrity and facilitating intercellular communication, although its direct role in coaggregation remains to be fully clarified. By integrating these perspectives, this review aims to elucidate how the proteosurfaceome and exoproteome influence bacterial coaggregation, offering insights into their combined impact on microbial community structure and function. Furthermore, we highlight existing knowledge gaps and propose directions for future research.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 108505"},"PeriodicalIF":12.1,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142852254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-06DOI: 10.1016/j.biotechadv.2024.108496
Jie Gu , Wanmeng Mu , Yan Xu , Yao Nie
The catalytic conversion of chiral alcohols and corresponding carbonyl compounds by carbonyl reductases (alcohol dehydrogenases), which are NAD(P) or NAD(P)H-dependent oxidoreductases, has attracted considerable attention. However, existing carbonyl reductases are insufficient to meet the demands of diverse industrial applications; hence, new enzymes with functions that can expand the toolbox of biocatalysts are urgently required. Developing precisely controlled chiral biocatalysts is of great significance for the efficient development of a broad spectrum of active pharmaceutical ingredients via biosynthesis. In this review, we summarized methods for discovering novel natural carbonyl reductases from various perspectives. Furthermore, advances in protein engineering, utilizing known sequence and structural information as well as catalytic dynamics mechanisms to improve potential functions, are also addressed. The exponential growth in data-driven tools over the past decade has made it possible to de novo design carbonyl reductases. Additionally, various applications of these high-performance carbonyl reductases and different strategies for coenzyme regeneration involving photocatalysis during the reaction process were reviewed. These advancements will bring new opportunities and challenges to the fields of green chemistry and biosynthesis in the future.
{"title":"From discovery to application: Enabling technology-based optimizing carbonyl reductases biocatalysis for active pharmaceutical ingredient synthesis","authors":"Jie Gu , Wanmeng Mu , Yan Xu , Yao Nie","doi":"10.1016/j.biotechadv.2024.108496","DOIUrl":"10.1016/j.biotechadv.2024.108496","url":null,"abstract":"<div><div>The catalytic conversion of chiral alcohols and corresponding carbonyl compounds by carbonyl reductases (alcohol dehydrogenases), which are NAD(P) or NAD(<em>P</em>)H-dependent oxidoreductases, has attracted considerable attention. However, existing carbonyl reductases are insufficient to meet the demands of diverse industrial applications; hence, new enzymes with functions that can expand the toolbox of biocatalysts are urgently required. Developing precisely controlled chiral biocatalysts is of great significance for the efficient development of a broad spectrum of active pharmaceutical ingredients via biosynthesis. In this review, we summarized methods for discovering novel natural carbonyl reductases from various perspectives. Furthermore, advances in protein engineering, utilizing known sequence and structural information as well as catalytic dynamics mechanisms to improve potential functions, are also addressed. The exponential growth in data-driven tools over the past decade has made it possible to de novo design carbonyl reductases. Additionally, various applications of these high-performance carbonyl reductases and different strategies for coenzyme regeneration involving photocatalysis during the reaction process were reviewed. These advancements will bring new opportunities and challenges to the fields of green chemistry and biosynthesis in the future.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 108496"},"PeriodicalIF":12.1,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794343","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 : 2024-12-06DOI: 10.1016/j.biotechadv.2024.108494
Ya-Nan Chen , You-Zhi Cui , Xiang-Rong Chen , Jun-Yi Wang , Bing-Zhi Li , Ying-Jin Yuan
Mining large-scale functional regions of the genome helps to understand the essence of cellular life. The rapid accumulation of genomic information provides a wealth of material for genomic functional, evolutionary, and structural research. DNA cloning technology is an important tool for understanding, analyzing, and manipulating the genetic code of organisms. As synthetic biologists engineer greater and broader genetic pathways and expand their research into new organisms, efficient tools capable of manipulating large-scale DNA will offer momentum to the ability to design, modify, and construct engineering life. In this review, we discuss the recent advances in the field of direct cloning of large genomic fragments, particularly of 50–150 kb genomic fragments. We specifically introduce the technological advances in the targeted release and capture steps of these cloning strategies. Additionally, the applications of large fragment cloning in functional genomics and natural product mining are also summarized. Finally, we further discuss the challenges and prospects for these technologies in the future.
{"title":"Direct cloning strategies for large genomic fragments: A review","authors":"Ya-Nan Chen , You-Zhi Cui , Xiang-Rong Chen , Jun-Yi Wang , Bing-Zhi Li , Ying-Jin Yuan","doi":"10.1016/j.biotechadv.2024.108494","DOIUrl":"10.1016/j.biotechadv.2024.108494","url":null,"abstract":"<div><div>Mining large-scale functional regions of the genome helps to understand the essence of cellular life. The rapid accumulation of genomic information provides a wealth of material for genomic functional, evolutionary, and structural research. DNA cloning technology is an important tool for understanding, analyzing, and manipulating the genetic code of organisms. As synthetic biologists engineer greater and broader genetic pathways and expand their research into new organisms, efficient tools capable of manipulating large-scale DNA will offer momentum to the ability to design, modify, and construct engineering life. In this review, we discuss the recent advances in the field of direct cloning of large genomic fragments, particularly of 50–150 kb genomic fragments. We specifically introduce the technological advances in the targeted release and capture steps of these cloning strategies. Additionally, the applications of large fragment cloning in functional genomics and natural product mining are also summarized. Finally, we further discuss the challenges and prospects for these technologies in the future.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 108494"},"PeriodicalIF":12.1,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784052","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 : 2024-12-05DOI: 10.1016/j.biotechadv.2024.108493
Ana F. Esteves , Ana L. Gonçalves , Vítor J.P. Vilar , José C.M. Pires
Microalgae, as photosynthetic microorganisms, offer a sustainable source of proteins, lipids, carbohydrates, pigments, vitamins, and antioxidants. Leveraging their advantages, such as fast growth, CO2 fixation, cultivation without arable land, and wastewater utilisation, microalgae can produce a diverse range of compounds. The extracted products find applications in bioenergy, animal feed, pharmaceuticals, nutraceuticals, cosmetics, and food industries. The selection of microalgal species is crucial, and their biochemical composition varies during growth phases influenced by environmental factors like light, salinity, temperature, and nutrients. Manipulating growth conditions shapes biomass composition, optimising the production of target compounds.
This review synthesises research from 2019 onwards, focusing on stress induction and two-stage cultivation in microalgal strategies. This review takes a broader approach, addressing the effects of various operating conditions on a range of biochemical compounds. It explores the impact of operational parameters (light, nutrient availability, salinity, temperature) on biomass composition, elucidating microalgal mechanisms. Challenges include species-specific responses, maintaining stable conditions, and scale-up complexities. A two-stage approach balances biomass productivity and compound yield. Overcoming challenges involves improving upstream and downstream processes, developing sophisticated monitoring systems, and conducting further modelling work. Future efforts should concentrate on strain engineering and refined monitoring, facilitating real-time adjustments for optimal compound accumulation. Moreover, conducting large-scale experiments is essential to evaluate the feasibility and sustainability of the process through techno-economic analysis and life cycle assessments.
{"title":"Is it possible to shape the microalgal biomass composition with operational parameters for target compound accumulation?","authors":"Ana F. Esteves , Ana L. Gonçalves , Vítor J.P. Vilar , José C.M. Pires","doi":"10.1016/j.biotechadv.2024.108493","DOIUrl":"10.1016/j.biotechadv.2024.108493","url":null,"abstract":"<div><div>Microalgae, as photosynthetic microorganisms, offer a sustainable source of proteins, lipids, carbohydrates, pigments, vitamins, and antioxidants. Leveraging their advantages, such as fast growth, CO<sub>2</sub> fixation, cultivation without arable land, and wastewater utilisation, microalgae can produce a diverse range of compounds. The extracted products find applications in bioenergy, animal feed, pharmaceuticals, nutraceuticals, cosmetics, and food industries. The selection of microalgal species is crucial, and their biochemical composition varies during growth phases influenced by environmental factors like light, salinity, temperature, and nutrients. Manipulating growth conditions shapes biomass composition, optimising the production of target compounds.</div><div>This review synthesises research from 2019 onwards, focusing on stress induction and two-stage cultivation in microalgal strategies. This review takes a broader approach, addressing the effects of various operating conditions on a range of biochemical compounds. It explores the impact of operational parameters (light, nutrient availability, salinity, temperature) on biomass composition, elucidating microalgal mechanisms. Challenges include species-specific responses, maintaining stable conditions, and scale-up complexities. A two-stage approach balances biomass productivity and compound yield. Overcoming challenges involves improving upstream and downstream processes, developing sophisticated monitoring systems, and conducting further modelling work. Future efforts should concentrate on strain engineering and refined monitoring, facilitating real-time adjustments for optimal compound accumulation. Moreover, conducting large-scale experiments is essential to evaluate the feasibility and sustainability of the process through techno-economic analysis and life cycle assessments.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 108493"},"PeriodicalIF":12.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-05DOI: 10.1016/j.biotechadv.2024.108497
Wenwen Yu , Ke Jin , Xianhao Xu , Yanfeng Liu , Jianghua Li , Guocheng Du , Jian Chen , Xueqin Lv , Long Liu
Generally, the metabolism in microbial organism is an intricate, spatiotemporal process that emerges from gene regulatory networks, which affects the efficiency of product biosynthesis. With the coming age of synthetic biology, spatiotemporal control systems have been explored as versatile strategies to promote product biosynthesis at both spatial and temporal levels. Meanwhile, the designer synthetic compartments provide new and promising approaches to engineerable spatiotemporal control systems to construct high-performance microbial cell factories. In this article, we comprehensively summarize recent developments in spatiotemporal control systems for tailoring advanced cell factories, and illustrate how to apply spatiotemporal control systems in different microbial species with desired applications. Future challenges of spatiotemporal control systems and perspectives are also discussed.
{"title":"Engineering microbial cell factories by multiplexed spatiotemporal control of cellular metabolism: Advances, challenges, and future perspectives","authors":"Wenwen Yu , Ke Jin , Xianhao Xu , Yanfeng Liu , Jianghua Li , Guocheng Du , Jian Chen , Xueqin Lv , Long Liu","doi":"10.1016/j.biotechadv.2024.108497","DOIUrl":"10.1016/j.biotechadv.2024.108497","url":null,"abstract":"<div><div>Generally, the metabolism in microbial organism is an intricate, spatiotemporal process that emerges from gene regulatory networks, which affects the efficiency of product biosynthesis. With the coming age of synthetic biology, spatiotemporal control systems have been explored as versatile strategies to promote product biosynthesis at both spatial and temporal levels. Meanwhile, the designer synthetic compartments provide new and promising approaches to engineerable spatiotemporal control systems to construct high-performance microbial cell factories. In this article, we comprehensively summarize recent developments in spatiotemporal control systems for tailoring advanced cell factories, and illustrate how to apply spatiotemporal control systems in different microbial species with desired applications. Future challenges of spatiotemporal control systems and perspectives are also discussed.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 108497"},"PeriodicalIF":12.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791161","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 : 2024-12-05DOI: 10.1016/j.biotechadv.2024.108495
David Medina-Ortiz , Ashkan Khalifeh , Hoda Anvari-Kazemabad , Mehdi D. Davari
Protein engineering through directed evolution and (semi)rational design has become a powerful approach for optimizing and enhancing proteins with desired properties. The integration of artificial intelligence methods has further accelerated protein engineering process by enabling the development of predictive models based on data-driven strategies. However, the lack of interpretability and transparency in these models limits their trustworthiness and applicability in real-world scenarios. Explainable Artificial Intelligence addresses these challenges by providing insights into the decision-making processes of machine learning models, enhancing their reliability and interpretability. Explainable strategies has been successfully applied in various biotechnology fields, including drug discovery, genomics, and medicine, yet its application in protein engineering remains underexplored. The incorporation of explainable strategies in protein engineering holds significant potential, as it can guide protein design by revealing how predictive models function, benefiting approaches such as machine learning-assisted directed evolution. This perspective work explores the principles and methodologies of explainable artificial intelligence, highlighting its relevance in biotechnology and its potential to enhance protein design. Additionally, three theoretical pipelines integrating predictive models with explainable strategies are proposed, focusing on their advantages, disadvantages, and technical requirements. Finally, the remaining challenges of explainable artificial intelligence in protein engineering and future directions for its development as a support tool for traditional protein engineering methodologies are discussed.
{"title":"Interpretable and explainable predictive machine learning models for data-driven protein engineering","authors":"David Medina-Ortiz , Ashkan Khalifeh , Hoda Anvari-Kazemabad , Mehdi D. Davari","doi":"10.1016/j.biotechadv.2024.108495","DOIUrl":"10.1016/j.biotechadv.2024.108495","url":null,"abstract":"<div><div>Protein engineering through directed evolution and (semi)rational design has become a powerful approach for optimizing and enhancing proteins with desired properties. The integration of artificial intelligence methods has further accelerated protein engineering process by enabling the development of predictive models based on data-driven strategies. However, the lack of interpretability and transparency in these models limits their trustworthiness and applicability in real-world scenarios. Explainable Artificial Intelligence addresses these challenges by providing insights into the decision-making processes of machine learning models, enhancing their reliability and interpretability. Explainable strategies has been successfully applied in various biotechnology fields, including drug discovery, genomics, and medicine, yet its application in protein engineering remains underexplored. The incorporation of explainable strategies in protein engineering holds significant potential, as it can guide protein design by revealing how predictive models function, benefiting approaches such as machine learning-assisted directed evolution. This perspective work explores the principles and methodologies of explainable artificial intelligence, highlighting its relevance in biotechnology and its potential to enhance protein design. Additionally, three theoretical pipelines integrating predictive models with explainable strategies are proposed, focusing on their advantages, disadvantages, and technical requirements. Finally, the remaining challenges of explainable artificial intelligence in protein engineering and future directions for its development as a support tool for traditional protein engineering methodologies are discussed.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 108495"},"PeriodicalIF":12.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-03DOI: 10.1016/j.biotechadv.2024.108492
Saber Imani , Shuojie Lv , Hongbo Qian , Yulan Cui , XiaoYan Li , Ali Babaeizad , Qingjing Wang
The prevalence of multidrug-resistant (MDR) ESKAPE pathogens, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa, represents a critical global public health challenge. In response, mRNA vaccines offer an adaptable and scalable platform for immunotherapy against ESKAPE pathogens by encoding specific antigens that stimulate B-cell-driven antibody production and CD8+ T-cell-mediated cytotoxicity, effectively neutralizing these pathogens and combating resistance. This review examines recent advancements and ongoing challenges in the development of mRNA vaccines targeting MDR ESKAPE pathogens. We explore antigen selection, the nuances of mRNA vaccine technology, and the complex interactions between bacterial infections and antibiotic resistance. By assessing the potential efficacy of mRNA vaccines and addressing key barriers to their paraclinical implementation, this review highlights the promising function of mRNA-based immunization in combating MDR ESKAPE pathogens.
{"title":"Current innovations in mRNA vaccines for targeting multidrug-resistant ESKAPE pathogens","authors":"Saber Imani , Shuojie Lv , Hongbo Qian , Yulan Cui , XiaoYan Li , Ali Babaeizad , Qingjing Wang","doi":"10.1016/j.biotechadv.2024.108492","DOIUrl":"10.1016/j.biotechadv.2024.108492","url":null,"abstract":"<div><div>The prevalence of multidrug-resistant (MDR) ESKAPE pathogens, including <em>Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa</em>, represents a critical global public health challenge. In response, mRNA vaccines offer an adaptable and scalable platform for immunotherapy against ESKAPE pathogens by encoding specific antigens that stimulate B-cell-driven antibody production and CD8<sup>+</sup> T-cell-mediated cytotoxicity, effectively neutralizing these pathogens and combating resistance. This review examines recent advancements and ongoing challenges in the development of mRNA vaccines targeting MDR ESKAPE pathogens. We explore antigen selection, the nuances of mRNA vaccine technology, and the complex interactions between bacterial infections and antibiotic resistance. By assessing the potential efficacy of mRNA vaccines and addressing key barriers to their paraclinical implementation, this review highlights the promising function of mRNA-based immunization in combating MDR ESKAPE pathogens.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 108492"},"PeriodicalIF":12.1,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-26DOI: 10.1016/j.biotechadv.2024.108491
Yangyang Hu , Guangyu Jiang , Yalun Wen , Yuchen Shao , Ge Yang , Feng Qu
Aptamers, as novel recognition molecules, hold immense potential across various domains such as biosensing, nucleic acid drugs, medical diagnostics, as well as environmental and food analysis. The majority of aptamer selection processes targeting small molecules and protein commonly employ magnetic bead-based methodologies, wherein the target is initially immobilized on magnetic beads, followed by magnetic separation. The Evolutionary Systematic Evolution of Ligands by Exponential Enrichment technique based on capillary electrophoresis (CE-SELEX) is acknowledged as one of the most efficient screening methods. Our research group has achieved breakthroughs in employing CE-SELEX for the selection of aptamers targeting small molecules. This paper outlines specific methodologies utilized from 2005 to 2023 for CE-SELEX screening for small-molecule targets. It summarizes the methods for the separation of small molecules and oligonucleotide complexes, as well as the identification of candidate aptamers. Drawing upon our research group's extensive experience in CE-SELEX for selecting aptamers targeting multi-scale targets, we offer strategic guidance specifically tailored to the screening of aptamers for small-molecule targets using CE-SELEX. This includes systematic insights into each technical aspect of the screening process: analysis of the structure of small-molecule targets and characteristics of ssDNA libraries, patterns of CE separation and collection of complexes, screening strategies, and CE-based methods for the affinity and specificity characterization of aptamers. This comprehensive review aims to contribute to the widespread adoption of CE-SELEX technology, enhancing the efficiency and success rate of selecting aptamers for small-molecule targets.
{"title":"Selection of aptamers targeting small molecules by capillary electrophoresis: Advances, challenges, and prospects","authors":"Yangyang Hu , Guangyu Jiang , Yalun Wen , Yuchen Shao , Ge Yang , Feng Qu","doi":"10.1016/j.biotechadv.2024.108491","DOIUrl":"10.1016/j.biotechadv.2024.108491","url":null,"abstract":"<div><div>Aptamers, as novel recognition molecules, hold immense potential across various domains such as biosensing, nucleic acid drugs, medical diagnostics, as well as environmental and food analysis. The majority of aptamer selection processes targeting small molecules and protein commonly employ magnetic bead-based methodologies, wherein the target is initially immobilized on magnetic beads, followed by magnetic separation. The Evolutionary Systematic Evolution of Ligands by Exponential Enrichment technique based on capillary electrophoresis (CE-SELEX) is acknowledged as one of the most efficient screening methods. Our research group has achieved breakthroughs in employing CE-SELEX for the selection of aptamers targeting small molecules. This paper outlines specific methodologies utilized from 2005 to 2023 for CE-SELEX screening for small-molecule targets. It summarizes the methods for the separation of small molecules and oligonucleotide complexes, as well as the identification of candidate aptamers. Drawing upon our research group's extensive experience in CE-SELEX for selecting aptamers targeting multi-scale targets, we offer strategic guidance specifically tailored to the screening of aptamers for small-molecule targets using CE-SELEX. This includes systematic insights into each technical aspect of the screening process: analysis of the structure of small-molecule targets and characteristics of ssDNA libraries, patterns of CE separation and collection of complexes, screening strategies, and CE-based methods for the affinity and specificity characterization of aptamers. This comprehensive review aims to contribute to the widespread adoption of CE-SELEX technology, enhancing the efficiency and success rate of selecting aptamers for small-molecule targets.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"78 ","pages":"Article 108491"},"PeriodicalIF":12.1,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142738184","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 : 2024-11-22DOI: 10.1016/j.biotechadv.2024.108481
Cheng Chen , Ya-Wen Li , Yuan-Yuan Zheng , Xiu-Juan Li , Na Wu , Qi Guo , Tian-Qiong Shi , He Huang
Genome engineering is extensively utilized in diverse scientific disciplines, advancing human welfare and addressing various challenges. Numerous genome engineering tools have been developed to modify genomic sequences. Among these, the CRISPR-Cas system has transformed the field and remains the most commonly employed genome-editing tool. However, the CRISPR-Cas system relies on induced double-strand breaks, with editing efficiency often limited by factors such as cell type and homologous recombination, impeding further progress. CRISPR-associated transposons (CASTs) represent programmable mobile genetic elements. CASTs identified as active were developed as CAST systems, which can perform RNA-guided DNA integration and are featured by high precision, programmability, and kilobase-level payload capacity. Moreover, CAST system allows for precise genome modifications independent of host DNA repair mechanisms, addressing the constraints of conventional CRISPR-Cas systems. It expands the genome engineering toolkit and is poised to become a representative of next-generation genome editing tools. This review thoroughly examines the research progress on CASTs, highlighting the current challenges faced in genome engineering based on CASTs, and offering insights into the ongoing development of this transformative technology.
{"title":"Expanding the frontiers of genome engineering: A comprehensive review of CRISPR-associated transposons","authors":"Cheng Chen , Ya-Wen Li , Yuan-Yuan Zheng , Xiu-Juan Li , Na Wu , Qi Guo , Tian-Qiong Shi , He Huang","doi":"10.1016/j.biotechadv.2024.108481","DOIUrl":"10.1016/j.biotechadv.2024.108481","url":null,"abstract":"<div><div>Genome engineering is extensively utilized in diverse scientific disciplines, advancing human welfare and addressing various challenges. Numerous genome engineering tools have been developed to modify genomic sequences. Among these, the CRISPR-Cas system has transformed the field and remains the most commonly employed genome-editing tool. However, the CRISPR-Cas system relies on induced double-strand breaks, with editing efficiency often limited by factors such as cell type and homologous recombination, impeding further progress. CRISPR-associated transposons (CASTs) represent programmable mobile genetic elements. CASTs identified as active were developed as CAST systems, which can perform RNA-guided DNA integration and are featured by high precision, programmability, and kilobase-level payload capacity. Moreover, CAST system allows for precise genome modifications independent of host DNA repair mechanisms, addressing the constraints of conventional CRISPR-Cas systems. It expands the genome engineering toolkit and is poised to become a representative of next-generation genome editing tools. This review thoroughly examines the research progress on CASTs, highlighting the current challenges faced in genome engineering based on CASTs, and offering insights into the ongoing development of this transformative technology.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"78 ","pages":"Article 108481"},"PeriodicalIF":12.1,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695054","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 : 2024-11-21DOI: 10.1016/j.biotechadv.2024.108482
Xiaoting Yu , Huiling Zhang , Tao Zhou , Kangliang Pan , Sayed Haidar Abbas Raza , Xing Shen , Hongtao Lei
Historically, antibodies have been divided into two functionally independent domains, the variable (V) region for antigen binding and the constant (C) region for mediating effector functions. However, this classical view of antibody function has been severely challenged by a large and growing number of studies, which reveal long-range conformational interactions and allosteric links between the V and C regions. This review comprehensively summarizes the existing studies on antibody allostery, including allosteric conformational changes induced by covalent modifications or noncovalent ligand binding. In addition, we discuss how intramolecular allosteric signals are transmitted from the V to C regions and vice versa. This review argues that there is sufficient evidence to revisit the structure-function relationship of antibodies. These advances in antibody allostery will provide a blueprint for regulating antibody functions in a simple and highly predictable manner. More focus on antibody allostery will definitely benefit antibody engineering and vaccine design in the field of biotechnology.
一直以来，抗体被划分为两个功能独立的结构域，可变区（V）用于抗原结合，恒定区（C）用于介导效应功能。然而，大量且日益增多的研究揭示了 V 区和 C 区之间的长程构象相互作用和异构联系，这对抗体功能的经典观点提出了严峻挑战。本综述全面总结了现有的抗体异构研究，包括共价修饰或非共价配体结合诱导的异构构象变化。此外，我们还讨论了分子内异构信号如何从 V 区传递到 C 区，反之亦然。这篇综述认为，有足够的证据可以重新审视抗体的结构-功能关系。抗体异构研究的这些进展将为以简单和高度可预测的方式调节抗体功能提供蓝图。对抗体异构的更多关注必将有利于生物技术领域的抗体工程和疫苗设计。
{"title":"A non-classical view of antibody properties: Allosteric effect between variable and constant regions","authors":"Xiaoting Yu , Huiling Zhang , Tao Zhou , Kangliang Pan , Sayed Haidar Abbas Raza , Xing Shen , Hongtao Lei","doi":"10.1016/j.biotechadv.2024.108482","DOIUrl":"10.1016/j.biotechadv.2024.108482","url":null,"abstract":"<div><div>Historically, antibodies have been divided into two functionally independent domains, the variable (V) region for antigen binding and the constant (C) region for mediating effector functions. However, this classical view of antibody function has been severely challenged by a large and growing number of studies, which reveal long-range conformational interactions and allosteric links between the V and C regions. This review comprehensively summarizes the existing studies on antibody allostery, including allosteric conformational changes induced by covalent modifications or noncovalent ligand binding. In addition, we discuss how intramolecular allosteric signals are transmitted from the V to C regions and <em>vice versa</em>. This review argues that there is sufficient evidence to revisit the structure-function relationship of antibodies. These advances in antibody allostery will provide a blueprint for regulating antibody functions in a simple and highly predictable manner. More focus on antibody allostery will definitely benefit antibody engineering and vaccine design in the field of biotechnology.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"78 ","pages":"Article 108482"},"PeriodicalIF":12.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695019","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}
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