Akbar Hasanzadeh , Sara Saeedi , Lida Dastanpour , Zahra S. Biabanaki , Leili Asadi , Hamid Noori , Michael R. Hamblin , Yong Liu , Mahdi Karimi
{"title":"Self-replicating nanomaterials as a new generation of smart nanostructures","authors":"Akbar Hasanzadeh , Sara Saeedi , Lida Dastanpour , Zahra S. Biabanaki , Leili Asadi , Hamid Noori , Michael R. Hamblin , Yong Liu , Mahdi Karimi","doi":"10.1016/j.biotechadv.2025.108565","DOIUrl":"10.1016/j.biotechadv.2025.108565","url":null,"abstract":"<div><div>Self-replication is the process by which a system or entity autonomously reproduces or generates copies of itself, transmitting hereditary information through its molecular structure. Self-replication can be attractive for various researchers, ranging from biologists focused on uncovering the origin of life, to synthetic chemists and nanotechnologists studying synthetic machines and nanorobots. The capability of a single structure to act as a template to produce multiple copies of itself could allow the bottom-up engineering of progressively complex reaction networks and nanoarchitectures from simple building blocks. Herein, we review nucleic acid-based and amino acid-based self-replicating systems and completely synthetic artificial systems and specially focused on specific aspects of self-replicating nanomaterials. We describe their mechanisms of action and provide a full discussion of the principal requirements for achieving nanostructures capable of self-replication.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"81 ","pages":"Article 108565"},"PeriodicalIF":12.1,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661856","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}
Jinling Yu , Cuili Li , Yajie Cheng , Shaobo Guo , Hongzhao Lu , Xiuchao Xie , Hao Ji , Yanming Qiao
{"title":"Mechanism and improvement of yeast tolerance to biomass-derived inhibitors: A review","authors":"Jinling Yu , Cuili Li , Yajie Cheng , Shaobo Guo , Hongzhao Lu , Xiuchao Xie , Hao Ji , Yanming Qiao","doi":"10.1016/j.biotechadv.2025.108562","DOIUrl":"10.1016/j.biotechadv.2025.108562","url":null,"abstract":"<div><div>Lignocellulosic biomass is regarded as a potentially valuable second-generation biorefinery feedstock. Yeast has the ability to metabolize this substrate and convert it into fuel ethanol and an array of other chemical products. Nevertheless, during the pretreatment of lignocellulosic biomass, inhibitors (furanaldehydes, carboxylic acids, phenolic compounds, etc.) are generated, which impede the growth and metabolic activities of yeast cells. Consequently, developing yeast strains with enhanced tolerance to these inhibitors is a crucial technological objective, as it can significantly enhance the efficiency of lignocellulosic biorefineries. This review provides a concise overview of the process of inhibitor generation and the detrimental effects of these inhibitors on yeast. It also summarizes the current state of research on the mechanisms of yeast tolerance to these inhibitors, focusing specifically on recent advances in enhancing yeast tolerance to these inhibitors by rational and non-rational strategies. Finally, it discusses the current challenges and future research directions.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"81 ","pages":"Article 108562"},"PeriodicalIF":12.1,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143637183","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}
Akila Wijerathna-Yapa , Kathy Sharon Isaac , Michelle Combe , Samuel Hume , Stanislav Sokolenko
{"title":"Re-imagining human cell culture media: Challenges, innovations, and future directions","authors":"Akila Wijerathna-Yapa , Kathy Sharon Isaac , Michelle Combe , Samuel Hume , Stanislav Sokolenko","doi":"10.1016/j.biotechadv.2025.108564","DOIUrl":"10.1016/j.biotechadv.2025.108564","url":null,"abstract":"<div><div>The development of optimized culture media is pivotal to advancements in human cell culture, underpinning progress in regenerative medicine, cell therapies, and personalized medicine. While foundational formulations like Eagle's Minimum Essential Medium (MEM) and Dulbecco's Modified Eagle Medium (DMEM) have historically enabled significant biological research, these media were primarily designed for non-human cells and do not adequately address the unique metabolic and functional requirements of human cells. This review examines the evolution of cell culture media, identifying persistent challenges in reproducibility, scalability, and ethical concerns, particularly regarding the reliance on animal-derived components such as fetal bovine serum (FBS).</div><div>We highlight innovations in serum-free and chemically defined media that offer promising alternatives by enhancing consistency, aligning with Good Manufacturing Practices, and addressing ethical concerns. Emerging approaches, including omics-based profiling, high-throughput screening, and artificial intelligence (AI)-driven media design, are reshaping media optimization by enabling precise tailoring to the needs of specific human cell types and patient-derived cells. Furthermore, we discuss economic and regulatory challenges, emphasizing the need for cost-effective and scalable solutions to facilitate clinical translation.</div><div>Looking forward, integrating advanced biotechnological tools such as 3D bioprinting, organ-on-a-chip systems, and personalized media formulations presents a transformative opportunity for human cell culture. These innovations, aligned with ethical and clinical standards, can drive the development of human-specific media systems that ensure reproducibility, scalability, and enhanced therapeutic potential, thereby advancing both research and clinical applications.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"81 ","pages":"Article 108564"},"PeriodicalIF":12.1,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655964","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}
Xu-Hong Li, Hui-Zhi Lu, Ji-Bao Yao, Chi Zhang, Tian-Qiong Shi, He Huang
{"title":"Recent advances in the application of CRISPR/Cas-based gene editing technology in Filamentous Fungi","authors":"Xu-Hong Li, Hui-Zhi Lu, Ji-Bao Yao, Chi Zhang, Tian-Qiong Shi, He Huang","doi":"10.1016/j.biotechadv.2025.108561","DOIUrl":"10.1016/j.biotechadv.2025.108561","url":null,"abstract":"<div><div>Filamentous fungi are essential industrial microorganisms that can serve as sources of enzymes, organic acids, terpenoids, and other bioactive compounds with significant applications in food, medicine, and agriculture. However, the underdevelopment of gene editing tools limits the full exploitation of filamentous fungi, which still present numerous untapped potential applications. In recent years, the CRISPR/Cas (clustered regularly interspaced short palindromic repeats) system, a versatile genome-editing tool, has advanced significantly and been widely applied in filamentous fungi, showcasing considerable research potential. This review examines the development and mechanisms of genome-editing tools in filamentous fungi, and contrasts the CRISPR/Cas9 and CRISPR/Cpf1 systems. The transformation and delivery strategies of the CRISPR/Cas system in filamentous fungi are also examined. Additionally, recent applications of CRISPR/Cas systems in filamentous fungi are summarized, such as gene disruption, base editing, and gene regulation. Strategies to enhance editing efficiency and reduce off-target effects are also highlighted, with the aim of providing insights for the future construction and optimization of CRISPR/Cas systems in filamentous fungi.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"81 ","pages":"Article 108561"},"PeriodicalIF":12.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143620599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genetic manipulations of brassinosteroid-related genes improve various agronomic traits and yield in cereals enabling new biotechnological revolution: Achievements and perspectives","authors":"Karolina Zolkiewicz, Sunny Ahmar, Damian Gruszka","doi":"10.1016/j.biotechadv.2025.108556","DOIUrl":"10.1016/j.biotechadv.2025.108556","url":null,"abstract":"<div><div>Brassinosteroids (BRs) are steroid phytohormones which regulate various developmental and physiological processes throughout plant life cycle, from seed development and germination, up to modulation of reproduction and senescence. Importantly, mutants defective in the BR biosynthesis or response show various degree of plant height reduction (dwarfism or semi-dwarfism). This agronomic trait is of particular importance considering that in contrast to tall cereal varieties, semi-dwarf cereal plants are more tolerant to lodging which occurs during unfavorable weather conditions and constitutes a serious threat to plant reproduction and yield. Moreover, it was shown that the BR deficiency or insensitivity lead to erect stature of cereal plants what enables increase in planting density and yield. The valuable combinations of these traits make the BR-related mutants exceptional alternatives in breeding programs. Noteworthy, BRs play a noticeable role in regulation of grain/kernel shape and size. Therefore, these crucial agronomic traits may be manipulated specifically in BR-dependent manner. Importantly, the semi-dwarf mutants have been successfully introduced into cereal breeding programs in the past, and new semi-dwarf mutants developed through application of gene editing approach have been recently reported as promising alternatives for development of novel, high-yielding cereal cultivars. This review presents a comprehensive description of genetic manipulations of the BR-related genes aimed at improvements of various agronomic traits in the major cereal crops - rice, wheat, maize, and barley. These improvements may be achieved through application of panicle- or grain-specific promoters, overexpression or gain-of-function approaches, gene silencing, and targeted gene editing.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"81 ","pages":"Article 108556"},"PeriodicalIF":12.1,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Recent advances in CRISPR-Cas system for Saccharomyces cerevisiae engineering","authors":"Xinxin Wu , Xiaowen Wan , Hongbin Yu , Huayi Liu","doi":"10.1016/j.biotechadv.2025.108557","DOIUrl":"10.1016/j.biotechadv.2025.108557","url":null,"abstract":"<div><div>Yeast <em>Saccharomyces cerevisiae</em> (<em>S. cerevisiae</em>) is a crucial industrial platform for producing a wide range of chemicals, fuels, pharmaceuticals, and nutraceutical ingredients. It is also commonly used as a model organism for fundamental research. In recent years, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) system has become the preferred technology for genetic manipulation in <em>S. cerevisiae</em> owing to its high efficiency, precision, and user-friendliness. This system, along with its extensive toolbox, has significantly accelerated the construction of pathways, enzyme optimization, and metabolic engineering in <em>S. cerevisiae</em>. Furthermore, it has allowed researchers to accelerate phenotypic evolution and gain deeper insights into fundamental biological questions, such as genotype-phenotype relationships. In this review, we summarize the latest advancements in the CRISPR-Cas toolbox for <em>S. cerevisiae</em> and highlight its applications in yeast cell factory construction and optimization, enzyme and phenotypic evolution, genome-scale functional interrogation, gene drives, and the advancement of biotechnologies. Finally, we discuss the challenges and potential for further optimization and applications of the CRISPR-Cas system in <em>S. cerevisiae</em>.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"81 ","pages":"Article 108557"},"PeriodicalIF":12.1,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143620598","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}
Jiaheng Liu , Yangyang Li , Xianhao Xu , Yaokang Wu , Yanfeng Liu , Jianghua Li , Guocheng Du , Jian Chen , Xueqin Lv , Long Liu
{"title":"Multiplexed engineering of cytochrome P450 enzymes for promoting terpenoid synthesis in Saccharomyces cerevisiae cell factories: A review","authors":"Jiaheng Liu , Yangyang Li , Xianhao Xu , Yaokang Wu , Yanfeng Liu , Jianghua Li , Guocheng Du , Jian Chen , Xueqin Lv , Long Liu","doi":"10.1016/j.biotechadv.2025.108560","DOIUrl":"10.1016/j.biotechadv.2025.108560","url":null,"abstract":"<div><div>Terpenoids, also known as isoprenoids, represent the largest and most structurally diverse family of natural products, and their biosynthesis is closely related to cytochrome P450 enzymes (P450s). Given the limitations of direct extraction from natural resources, such as low productivity and environmental concerns, heterologous expression of P450s in microbial cell factories has emerged as a promising, efficient, and sustainable strategy for terpenoid production. The yeast expression system is a preferred selection for terpenoid synthesis because of its inner membrane system, which is required for eukaryotic P450 expression, and the inherent mevalonate pathway providing precursors for terpenoid synthesis. In this review, we discuss the advanced strategies used to enhance the local enzyme concentration and catalytic properties of P450s in <em>Saccharomyces cerevisiae</em>, with a focus on recent developments in metabolic and protein engineering. Expression enhancement and subcellular compartmentalization are specifically employed to increase the local enzyme concentration, whereas cofactor, redox partner, and enzyme engineering are utilized to improve the catalytic efficiency and substrate specificity of P450s. Subsequently, we discuss the application of P450s for the pathway engineering of terpenoid synthesis and whole-cell biotransformation, which are profitable for the industrial application of P450s in <em>S. cerevisiae</em> chassis. Finally, we explore the potential of using computational and artificial intelligence technologies to rationally design and construct high-performance cell factories, which offer promising pathways for future terpenoid biosynthesis.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"81 ","pages":"Article 108560"},"PeriodicalIF":12.1,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143600647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mapping the architecture of animal toxin systems by mass spectrometry imaging","authors":"Maik Damm , Andreas Vilcinskas , Tim Lüddecke","doi":"10.1016/j.biotechadv.2025.108548","DOIUrl":"10.1016/j.biotechadv.2025.108548","url":null,"abstract":"<div><div>Animal toxins are proteins, peptides or metabolites that cause negative effects against predators, prey or competitors following contact or injection. They work by interacting with enzymes, receptors and other targets causing pain, debilitation or leading even to death. Their biological significance and pharmacological effects in humans make them interesting to researchers, but much remains to be learned about their mechanisms of action, storage, tissue-specific distribution and maturation. Mass spectrometry imaging (MSI), a technique that determines the spatial distribution of molecules based on their molecular mass, is uniquely positioned to answer these key questions and pioneering studies have already confirmed its potential impact on the field of zootoxinology. We provide the first comprehensive review of MSI as a means to study animal toxins, the lessons learned thus far, and potential future applications. This fills an important gap in the literature and will facilitate future work on the structure, function, evolutionary history and medical uses of animal toxins.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"81 ","pages":"Article 108548"},"PeriodicalIF":12.1,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143563442","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}
Hua-Wei Lv , Jia-Gui Tang , Bin Wei , Meng-Di Zhu , Hua-Wei Zhang , Zhong-Bo Zhou , Bo-Yi Fan , Hong Wang , Xing-Nuo Li
{"title":"Bioinformatics assisted construction of the link between biosynthetic gene clusters and secondary metabolites in fungi","authors":"Hua-Wei Lv , Jia-Gui Tang , Bin Wei , Meng-Di Zhu , Hua-Wei Zhang , Zhong-Bo Zhou , Bo-Yi Fan , Hong Wang , Xing-Nuo Li","doi":"10.1016/j.biotechadv.2025.108547","DOIUrl":"10.1016/j.biotechadv.2025.108547","url":null,"abstract":"<div><div>Fungal secondary metabolites are considered as important resources for drug discovery. Despite various methods being employed to facilitate the discovery of new fungal secondary metabolites, the trend of identifying novel secondary metabolites from fungi is inevitably slowing down. Under laboratory conditions, the majority of biosynthetic gene clusters, which store information for secondary metabolites, remain inactive. Therefore, establishing the link between biosynthetic gene clusters and secondary metabolites would contribute to understanding the genetic logic underlying secondary metabolite biosynthesis and alleviating the current challenges in discovering novel natural products. Bioinformatics methods have garnered significant attention due to their powerful capabilities in data mining and analysis, playing a crucial role in various aspects. Thus, we have summarized successful cases since 2016 in which bioinformatics methods were utilized to establish the link between fungal biosynthetic gene clusters and secondary metabolites, focusing on their biosynthetic gene clusters and associated secondary metabolites, with the goal of aiding the field of natural product discovery.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"81 ","pages":"Article 108547"},"PeriodicalIF":12.1,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536403","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}
Xu Liu , Helen Park , Yannic Sebastian Ackermann , Luc Avérous , Hendrik Ballerstedt , Werner Besenmatter , Blas Blázquez , Uwe T. Bornscheuer , Yannick Branson , William Casey , Víctor de Lorenzo , Weiliang Dong , Tilman Floehr , Manuel S. Godoy , Yu Ji , Andreas Jupke , Jürgen Klankermayer , David San León , Luo Liu , Xianrui Liu , Guo-Qiang Chen
{"title":"Exploring biotechnology for plastic recycling, degradation and upcycling for a sustainable future","authors":"Xu Liu , Helen Park , Yannic Sebastian Ackermann , Luc Avérous , Hendrik Ballerstedt , Werner Besenmatter , Blas Blázquez , Uwe T. Bornscheuer , Yannick Branson , William Casey , Víctor de Lorenzo , Weiliang Dong , Tilman Floehr , Manuel S. Godoy , Yu Ji , Andreas Jupke , Jürgen Klankermayer , David San León , Luo Liu , Xianrui Liu , Guo-Qiang Chen","doi":"10.1016/j.biotechadv.2025.108544","DOIUrl":"10.1016/j.biotechadv.2025.108544","url":null,"abstract":"<div><div>The persistent demand for plastic commodities, inadequate recycling infrastructure, and pervasive environmental contamination due to plastic waste present a formidable global challenge. Recycling, degradation and upcycling are the three most important ways to solve the problem of plastic pollution. Sequential enzymatic and microbial degradation of mechanically and chemically pre-treated plastic waste can be orchestrated, followed by microbial conversion into value-added chemicals and polymers through mixed culture systems. Furthermore, plastics-degrading enzymes can be optimized through protein engineering to enhance their specific binding capacities, stability, and catalytic efficiency across a broad spectrum of polymer substrates under challenging high salinity and temperature conditions. Also, the production and formulation of enzyme mixtures can be fine-tuned to suit specific waste compositions, facilitating their effective deployment both in vitro, in vivo and in combination with chemical technologies. Here, we emphasized the comprehensive strategy leveraging microbial processes to transform mixed plastics of fossil-derived polymers such as PP, PE, PU, PET, and PS, most notably polyesters, in conjunction with potential biodegradable alternatives such as PLA and PHA. Any residual material resistant to enzymatic degradation can be reintroduced into the process loop following appropriate physicochemical treatment.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"81 ","pages":"Article 108544"},"PeriodicalIF":12.1,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536408","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}