{"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}
{"title":"Expanding the cryoprotectant toolbox in biomedicine by multifunctional antifreeze peptides","authors":"Shiva Hemmati","doi":"10.1016/j.biotechadv.2025.108545","DOIUrl":"10.1016/j.biotechadv.2025.108545","url":null,"abstract":"<div><div>The global cryopreservation market size rises exponentially due to increased demand for cell therapy-based products, assisted reproductive technology, and organ transplantation. Cryoprotectants (CPAs) are required to reduce ice-related damage, osmotic cell injury, and protein denaturation. Antioxidants are needed to hamper membrane lipid peroxidation under freezing stress, and antibiotics are added to the cryo-solutions to prevent contamination. The vitrification process for sized organs requires a high concentration of CPA, which is hardly achievable using conventional penetrating toxic CPAs like DMSO. Antifreeze peptides (AFpeps) are biocompatible CPAs leveraging inspiration from nature, such as freeze-tolerant and freeze-avoidant organisms, to circumvent logistic limitations in cryogenic conditions. This study aims to introduce the advances of AFpeps with cell-penetrating, antioxidant, and antimicrobial characteristics. We herein revisit the placement of AFpeps in the biobanking of cancer cells, immune cells, stem cells, blood cells, germ cells (sperms and oocytes), and probiotics. Implementing low-immunogenic AFpeps for allograft cryopreservation minimizes HLA mismatching risk after organ transplantation. Applying AFpeps to formulate bioinks with optimal rheology in extrusion-based 3D cryobiopriners expedites the bench-to-beside transition of bioprinted scaffolds. This study advocates that the fine-tuned synthetic or insect-derived AFpeps, forming round blunt-shape crystals, are biomedically broad-spectrum, and cell-permeable AFpeps from marine and plant sources, which result in sharp ice crystals, are appropriate for cryosurgery. Perspectives of the available room for developing peptide mimetics in favor of higher activity and stability and peptide-functionalized nanoparticles for enhanced delivery are delineated. Finally, antitumor immune activation by cryoimmunotherapy as an autologous in-vivo tumor lysate vaccine has been illustrated.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"81 ","pages":"Article 108545"},"PeriodicalIF":12.1,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536406","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}
Ziying Yao , Taiqing Liu , Jingwen Wang , Yunhai Fu , Jinhua Zhao , Xiaoyu Wang , Yinqi Li , Xiaodong Yang , Zhiyao He
{"title":"Targeted delivery systems of siRNA based on ionizable lipid nanoparticles and cationic polymer vectors","authors":"Ziying Yao , Taiqing Liu , Jingwen Wang , Yunhai Fu , Jinhua Zhao , Xiaoyu Wang , Yinqi Li , Xiaodong Yang , Zhiyao He","doi":"10.1016/j.biotechadv.2025.108546","DOIUrl":"10.1016/j.biotechadv.2025.108546","url":null,"abstract":"<div><div>As an emerging therapeutic tool, small interfering RNA (siRNA) had the capability to down-regulate nearly all human mRNAs via sequence-specific gene silencing. Numerous studies have demonstrated the substantial potential of siRNA in the treatment of broad classes of diseases. With the discovery and development of various delivery systems and chemical modifications, six siRNA-based drugs have been approved by 2024. The utilization of siRNA-based therapeutics has significantly propelled efforts to combat a wide array of previously incurable diseases and advanced at a rapid pace, particularly with the help of potent targeted delivery systems. Despite encountering several extracellular and intracellular challenges, the efficiency of siRNA delivery has been gradually enhanced. Currently, targeted strategies aimed at improving potency and reducing toxicity played a crucial role in the druggability of siRNA. This review focused on recent advancements on ionizable lipid nanoparticles (LNPs) and cationic polymer (CP) vectors applied for targeted siRNA delivery. Based on various types of targeted modifications, we primarily described delivery systems modified with receptor ligands, peptides, antibodies, aptamers and amino acids. Finally, we discussed the challenges and opportunities associated with siRNA delivery systems based on ionizable LNPs and CPs vectors.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"81 ","pages":"Article 108546"},"PeriodicalIF":12.1,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522534","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}
Weizhu Zeng , Hongbiao Li , Shike Liu , Zhengshan Luo , Jian Chen , Jingwen Zhou
{"title":"Biosynthesis and bioactivities of triterpenoids from Centella asiatica: Challenges and opportunities","authors":"Weizhu Zeng , Hongbiao Li , Shike Liu , Zhengshan Luo , Jian Chen , Jingwen Zhou","doi":"10.1016/j.biotechadv.2025.108541","DOIUrl":"10.1016/j.biotechadv.2025.108541","url":null,"abstract":"<div><div><em>Centella asiatica</em> (L.) Urban is an herbaceous perennial plant that has long been widely used in traditional medicine, due to its diverse wound-healing, neuroprotection, antioxidant and anti-inflammatory properties. The major functional bioactive secondary metabolites are the triterpenoids asiatic acid, madecassic acid, asiaticoside and madecassoside, collectively known as centellosides. Current extraction methods for <em>C. asiatica</em> are unable to meet market demand for extracts and pure functional components. Biotechnological approaches based on synthetic biology and microbial cell factories are a promising alternative. This review summarises the major secondary metabolites and their biological activities, and the biosynthetic pathway of functional triterpenoids in <em>C. asiatica.</em> Biotechnological production of centellosides is also described, including <em>in vitro</em> plant cultures and construction of microbial cell factories. Finally, current challenges and future perspectives for sustainable production of centellosides are discussed, and guidelines for future engineering are proposed.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"80 ","pages":"Article 108541"},"PeriodicalIF":12.1,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143454927","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":"Alpha-ketoacid decarboxylases: Diversity, structures, reaction mechanisms, and applications for biomanufacturing of platform chemicals and fuels","authors":"Khanh Ha , Seunghyun Ryu , Cong T. Trinh","doi":"10.1016/j.biotechadv.2025.108531","DOIUrl":"10.1016/j.biotechadv.2025.108531","url":null,"abstract":"<div><div>In living cells, alpha-ketoacid decarboxylases (KDCs, EC 4.1.1.-) are a class of enzymes that convert alpha-ketoacids into aldehydes through decarboxylation. These aldehydes serve as either drop-in chemicals or precursors for the biosynthesis of alcohols, carboxylic acids, esters, and alkanes. These compounds play crucial roles in cellular metabolism and fitness and the bioeconomy, facilitating the sustainable and renewable biomanufacturing of platform chemicals and fuels. This review explores the diversity and classification of KDCs, detailing their structures, mechanisms, and functions. We highlight recent advancements in repurposing KDCs to enhance their efficiency and robustness for biomanufacturing. Additionally, we present modular KDC-dependent metabolic pathways for the microbial biosynthesis of aldehydes, alcohols, carboxylic acids, esters, and alkanes. Finally, we discuss recent developments in the modular cell engineering technology that can potentially be applied to harness the diversity of KDC-dependent pathways for biomanufacturing platform chemicals and fuels.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"81 ","pages":"Article 108531"},"PeriodicalIF":12.1,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143424944","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}