Biotechnology advances最新文献

{"title":"Exploring the enzymatic landscape of 4-α-glucanotransferases in carbohydrate bioprocessing","authors":"Yu Wang ,&nbsp;Yu Tian ,&nbsp;Marie Sofie Møller ,&nbsp;Zhengyu Jin ,&nbsp;Xiaoxiao Li ,&nbsp;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":"2026-01-01","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}

{"title":"Environments contaminated by pesticides are hotspots for the selection of bacterial chassis for biotechnological applications","authors":"Caroline Rosa Silva ,&nbsp;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":"2026-01-01","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}

{"title":"Accelerated adaptive laboratory evolution: A tool for evolutionary biotechnology","authors":"Luna Declerck ,&nbsp;Florent Bouchon ,&nbsp;Wouter Demeester ,&nbsp;Chiara Guidi ,&nbsp;Marjan De Mey","doi":"10.1016/j.biotechadv.2025.108741","DOIUrl":"10.1016/j.biotechadv.2025.108741","url":null,"abstract":"<div><div>Adaptive laboratory evolution (ALE) is a powerful strategy for enhancing microbial traits by harnessing the principles of natural selection in controlled environments. It has enabled significant advances in microbial growth, stress tolerance, and product yield across a variety of organisms, while also providing insight into evolutionary mechanisms. However, the traditional ALE workflow is time- and resource-intensive, relying on prolonged cultivation to allow beneficial mutations to emerge and be maintained in the population. To improve this, a range of evolutionary engineering tools have been developed to accelerate ALE by increasing mutation rates and genetic diversity in evolving strains. In this review, we explore the core parameters that shape ALE, such as selection pressure, transfer method, and passage size, and provide a comprehensive overview of both established and emerging acceleration methods. These techniques are categorized based on portability (applicability across different microorganisms), genomic targetability (specificity of mutagenesis), and reliability (minimal off-target mutations and mutational reproducibility), with the resulting framework for selecting the most suitable approach summarized in Table 3 at the end of the review. We highlight the growing potential of accelerated ALE and outline future directions, including the integration of genome-wide and targeted mutagenesis, computational modeling, laboratory automation, and broader application beyond model organisms. This review aims to streamline the use of accelerated ALE, unlocking its true potential for advancing microbial strain engineering.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108741"},"PeriodicalIF":12.5,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145367457","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":"Advances in biosensors for microbial biosynthesis of amino acids and their derivatives","authors":"Huina Dong ,&nbsp;Tingting Li ,&nbsp;Xinyi Ren ,&nbsp;Huiying Wang ,&nbsp;Xuan Liu ,&nbsp;Xuyang Huang ,&nbsp;Xiaolin Shen ,&nbsp;Gang Fu ,&nbsp;Miaomiao Xia ,&nbsp;Guangqing Du ,&nbsp;Xinxiao Sun ,&nbsp;Jia Wang ,&nbsp;Zhaoxia Jin ,&nbsp;Sang Yup Lee ,&nbsp;Qipeng Yuan ,&nbsp;Dawei Zhang","doi":"10.1016/j.biotechadv.2025.108746","DOIUrl":"10.1016/j.biotechadv.2025.108746","url":null,"abstract":"<div><div>Amino acids and their derivatives play pivotal roles across diverse fields including biotechnology, pharmaceuticals, agriculture, and industrial manufacturing. The development of high-throughput screening methods for strains producing amino acids and their derivatives is crucial for both mining key enzymes and screening overproducers. This review systematically evaluates six classes of direct biosensors employed in the metabolic engineering of amino acid- or derivative-producing strains. These include biosensors based on transcription factors, riboswitches, Förster resonance energy transfer, circularly permuted fluorescent proteins, compound-inducible putative promoter regions, and protein translation elements. Their operational principles and recent advances in rational design, performance optimization, and practical implementation are critically analyzed. In addition, a systematic analysis of four categories of indirect biosensing strategies for the screening or regulation of amino acid- or derivative-producing strains is provided. These strategies target universal metabolic precursors, pathway-specific precursors, enzymatically transformed downstream metabolites, or competitive intermediates in branched pathways. Then, the design strategies, performance optimization methods, and practical implementation challenges of the existing biosensors are compared, which are accompanied by the discussion of the key parameters that are optimal for the biosensors applied in metabolic engineering. This work will facilitate the development of biosensors for metabolites that currently lack biosensing systems, and promote the innovation of the existing biosensors. These developments are expected to support efficient and sustainable production of amino acid-related compounds and other high-value metabolites.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108746"},"PeriodicalIF":12.5,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145383252","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":"Gene expression and protein abundance: Just how associated are these molecular traits?","authors":"Anahita Samih ,&nbsp;Maurício Alexander de Moura Ferreira ,&nbsp;Zoran Nikoloski","doi":"10.1016/j.biotechadv.2025.108720","DOIUrl":"10.1016/j.biotechadv.2025.108720","url":null,"abstract":"<div><div>The ability to accurately predict the abundance of proteins from the expression of the corresponding genes has enormous potential for the advancement of biotechnological applications using metabolic engineering and synthetic biology approaches. Addressing this problem has been challenging because of the lag in methodological advances in quantifying protein abundances. Here, we reviewed and classified studies that investigated the relationship between gene expression and protein abundance in different experimental settings and cellular contexts. We focused on comparing and contrasting the findings based on different correlation-based measures, widely used with nominal or transformed transcriptomics and proteomics data. We also included studies that investigated and attempted to explain the observed correlations between gene expression and protein abundance by incorporating data on additional factors, such as translation rate, protein degradation, and post-transcriptional modifications, using various statistical and mechanistic modelling frameworks. Finally, we provided an overview of how the latest advances using data from single-cell analyses have contributed to addressing this pressing question. Our review offers a perspective about how the findings about the relationship between gene expression and protein abundance can propel biotechnological advances, particularly focusing on opportunities resulting from the availability of protein-constrained metabolic models and the complementary machine and deep learning models.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108720"},"PeriodicalIF":12.5,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211524","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":"From IscB to Cas9: Engineering and advances in the next generation of miniature gene editing tools","authors":"Changli Zhou ,&nbsp;Sisi Zhu ,&nbsp;Chengjian Luo ,&nbsp;Wenju Wang ,&nbsp;Huiqin Fan ,&nbsp;Yuan Gao ,&nbsp;Xinde Xu ,&nbsp;QiuYan Wang ,&nbsp;Yu You ,&nbsp;Tian Xie","doi":"10.1016/j.biotechadv.2025.108743","DOIUrl":"10.1016/j.biotechadv.2025.108743","url":null,"abstract":"<div><div>The CRISPR-Cas system, distinguished by its inherent modularity and broad programmability, has catalyzed a paradigm shift in genome engineering due to its unprecedented accuracy, specificity, and on-target efficiency, now serving as the cornerstone of modern genome manipulation. The efficient delivery of gene editing tools remains a major technical hurdle to clinical application, primarily due to the lack of compact editors. The recent identification of the transposon-associated nuclease IscB as an evolutionary ancestor of Cas9 has provided important insights into the molecular evolution of the CRISPR–Cas9 system. Notably, IscB is a highly compact nuclease, approximately one-third the size of Cas9, capable of precise nucleic acid cleavage in eukaryotic cells under the guidance of ωRNA. These features make it a promising candidate for the development of next-generation miniaturized genome editors. However, natural IscB exhibits limited editing performance in eukaryotic systems.</div><div>This review first outlines the biochemical function of the transposon IscB and briefly traces the evolutionary origin of the Cas9 system. It then describes and compares the structural characteristics and cleavage mechanisms of OgeuIscB and Cas9. Subsequent sections summarize various engineering strategies for current IscB systems, including the development of base editors and recent advances in their application. Finally, the limitations of existing systems are discussed, and potential directions for future optimization are proposed, aiming to provide new insights and facilitate the advancement of IscB-based miniaturized editors.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108743"},"PeriodicalIF":12.5,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145343025","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":"Microbial quorum sensing: Mechanisms, applications, and challenges","authors":"Qi Ruan ,&nbsp;Shuting Geng ,&nbsp;Jianqiu Yu ,&nbsp;Leilei Lu ,&nbsp;Yanhua Liu ,&nbsp;Jianqiu Chen ,&nbsp;Qianjiahua Liao ,&nbsp;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":"2026-01-01","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}

{"title":"Adaptability and resiliency of Lepidoptera and their cells in culture - linking evolutionary biology to biotechnological advantage","authors":"Sophia Letcher ,&nbsp;Barry Trimmer ,&nbsp;David L. Kaplan","doi":"10.1016/j.biotechadv.2025.108721","DOIUrl":"10.1016/j.biotechadv.2025.108721","url":null,"abstract":"<div><div>Lepidopteran cells are an important tool for producing recombinant proteins, vaccines, and other biomolecules, and there is growing interest in using lepidopteran cells for other industries such as cultivated meat or as bioactuators. Lepidopteran cells are favored over mammalian cells for these applications because they grow in relatively simple systems in low-cost culture media and are adaptable to a wide range of culture conditions. Although these advantages of lepidopteran cells are well known, the mechanistic basis for these advantages are not well understood. Here, we consider the evolutionary and physiological pressures guiding cell-level adaptations in Lepidoptera and how these adaptations lead to favorable cell culture behavior. Specifically, we link lepidopteran cell resiliency (i.e., ability to withstand environmental stressors) with a robust antioxidant system, altered chromosome structure, polyploidy, and pre-conditioning of cell stress pathways. We also link lepidopteran cell adaptability (i.e., ability to grow in a range of media formulations) to metabolic flexibility, variable resource allocation options and efficient energy budgeting. We then consider the evolutionary pressures that led to selection for these favorable cell culture traits, including exposure to high oxidative stress, environmental clastogens, small size, metamorphosis, and limited food access and diversity. Finally, we highlight key future experiments to facilitate an improved understanding of lepidopteran resiliency and adaptability for biomanufacturing goals with insect cells, as well as ideas for utilizing this knowledge to improve vertebrate cell culture.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108721"},"PeriodicalIF":12.5,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145224864","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":"Material-binding peptides: sources, mechanisms, directed evolution and applications","authors":"Huan Chen ,&nbsp;Ya-Ting Gao ,&nbsp;Xu-Zhe Ge ,&nbsp;Xin Wang ,&nbsp;Feng Cheng ,&nbsp;Ya-Ping Xue ,&nbsp;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":"2026-01-01","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}

{"title":"Smart culture medium optimization for recombinant protein production: Experimental, modeling, and AI/ML-driven strategies","authors":"Galib Khan ,&nbsp;Carrie Sanford ,&nbsp;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":"2026-01-01","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}