Biotechnology advances最新文献

{"title":"Challenges of polyethylene (PE) biodegradation – A perspective","authors":"Luo Liu ,&nbsp;Mengxin Zhang ,&nbsp;Haijun Xu ,&nbsp;Zvjezdana Findrik Blažević ,&nbsp;Hendrik Ballerstedt ,&nbsp;Lars M. Blank","doi":"10.1016/j.biotechadv.2025.108717","DOIUrl":"10.1016/j.biotechadv.2025.108717","url":null,"abstract":"<div><div>PE brings convenience to people, as this plastic is cheap and performs in thousands of different forms. As PE with its high molecular weight and its stable C<img>C bonds is recalcitrant. For decades, much work has been dedicated to screening microorganisms isolated from, e.g., soil, water, landfills, complemented with microbes from strain collections for their potential to degrade PE. However, no convincing evidence of the biodegradation of high molecular weight PE, without any pretreatment, has been presented so far. Here, we discuss potential mechanisms of PE biodegradation, especially the activation of the C-C-bond by specific or non-specific oxygenation reactions. We argue that it is doubtful that any enzyme can accept a non-water soluble, high molecular weight polymer in its highly oxidative active side. Hence, reactive oxygen species (ROS) could be a critical step toward biodegradation. Investigating the process of oxygenation may help to unravel the mystery of PE (bio)degradation. In this context, we further argue that reliable analytical methods are necessary, including stable and maybe even radioactive isotope-labelled polymers, to avoid ambiguous experimental results.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"85 ","pages":"Article 108717"},"PeriodicalIF":12.5,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093952","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":"Microfluidics in biomanufacturing process development","authors":"Federico Moreno-Sibaja,&nbsp;Da Zou,&nbsp;Sha Liu,&nbsp;Chun-Xia Zhao,&nbsp;Lukas Gerstweiler","doi":"10.1016/j.biotechadv.2025.108715","DOIUrl":"10.1016/j.biotechadv.2025.108715","url":null,"abstract":"<div><div>Biomanufacturing processes are expanding their capabilities due to an increasing demand for high-value products, chemicals, biofuels, and food. Recent trends in bioprocess development focus on scale down systems during early-stage to enable rapid and cost-effective experimentation. Microfluidic systems are powerful alternatives for biomanufacturing process development by enabling dynamic and high-throughput experiments, enhanced process control, and reduced operational volumes and times. Microfluidic setups are applied across the entire bioprocessing workflow, from upstream tasks such as strain development and cell growth to downstream processes including cell lysis and purification. The integration of sensors and automation are critical for obtaining high-quality data, which is key for process optimization and scale-up. This review summarizes the fundamentals of microfluidics, highlighting key features of this technology for biomanufacturing process development. The application of microfluidic systems for upstream and downstream processing optimization and scale-up are then discussed. Finally, challenges and future perspectives are presented, specifically fabrication technologies, automation, and artificial intelligence.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"85 ","pages":"Article 108715"},"PeriodicalIF":12.5,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145085160","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":"Loop engineering in enzymes from structure to function: Mechanisms, methodologies, and engineering strategies","authors":"Chenshuo Song ,&nbsp;Jie Gu ,&nbsp;Hanwen Ren ,&nbsp;Ziyi Li ,&nbsp;Dingyu Xie ,&nbsp;Laichuang Han ,&nbsp;Jun Qiao ,&nbsp;Zhongyi Cheng ,&nbsp;Yao Nie ,&nbsp;Zhemin Zhou","doi":"10.1016/j.biotechadv.2025.108716","DOIUrl":"10.1016/j.biotechadv.2025.108716","url":null,"abstract":"<div><div>Enzymes play indispensable roles not only in biological processes but also in industrial applications such as chemical manufacturing, food processing, and medicine. The loop, contrasting with the rigid conformations of α-helices and β-sheets, significantly influences the catalytic performance and environmental adaptability due to its structural and conformational diversity. Given this flexibility, loop engineering emerges as a key strategy to modulate enzyme properties. This review aims to provide a systematic overview of loop functions and their engineering. Specifically, it (1) summarizes the physiological functions associated with key loops, (2) elucidates the underlying molecular mechanisms, (3) outlines current experimental and computational methodologies for loop investigation, and (4) compiles state-of-the-art strategies for loop engineering. The novelty of this review lies in its comprehensive synthesis of recent advances and practical applications specifically focused on loop research, an area crucial for understanding protein structure-function relationships but often less emphasized than other secondary structures. Therefore, a systematic introduction to loops through this review is of great significance for understanding the structure-function relationships of proteins and enhancing enzyme performance.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"85 ","pages":"Article 108716"},"PeriodicalIF":12.5,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079572","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":"Plant cell wall biosynthesis: Immune signaling, genome editing, and physiological implications for biomass valorization","authors":"Nisar Uddin ,&nbsp;Muhammad Wajid Ullah ,&nbsp;Kaihuai Li ,&nbsp;Fengquan Liu ,&nbsp;Xin Xie","doi":"10.1016/j.biotechadv.2025.108714","DOIUrl":"10.1016/j.biotechadv.2025.108714","url":null,"abstract":"<div><div>Plants continuously face biotic stress from pathogens, pests, and environmental challenges that threaten their survival and productivity. In response, plants have developed complex immune systems, with the cell wall playing a central role in defense. The plant cell wall not only provides mechanical strength but also acts as a dynamic barrier against pathogens, influencing both plant growth and immune responses. This review discusses the molecular mechanisms of cell wall biosynthesis, facilitated by multi-omics technologies, particularly the synthesis and regulation of lignin and other polysaccharides, which contribute to cell wall integrity and plant immunity. It explores the interplay between cell wall modifications and immune signaling pathways, highlighting the role of pattern recognition receptors in pathogen detection and defense activation. Additionally, the potential of genome editing, especially CRISPR-Cas, in enhancing cell wall characteristics to improve pathogen resistance and biomass utilization is discussed. With growing interest in lignocellulosic biomass as a renewable resource for biofuels and bioproducts, this review also addresses the challenges of biomass recalcitrance, focusing on biotechnological advancements to improve saccharification efficiency. Finally, the review proposes integrated strategies combining genetic modifications, biotechnological innovations, and sustainable practices to optimize lignocellulosic biomass for a bio-based economy, contributing to both agricultural resilience and sustainable energy production. As climate change accelerates, these technologies hold the promise of developing resilient crops and enhancing the capacity of the bioeconomy to mitigate environmental impacts.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"85 ","pages":"Article 108714"},"PeriodicalIF":12.5,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145063544","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":"Genetically engineered Escherichia coli: The new recyclers of PET plastic waste","authors":"Chengyong Wang ,&nbsp;Jie Zhang ,&nbsp;Zhi Zhou ,&nbsp;Ling Jiang","doi":"10.1016/j.biotechadv.2025.108713","DOIUrl":"10.1016/j.biotechadv.2025.108713","url":null,"abstract":"<div><div>Polyethylene terephthalate (PET) pollution is a significant environmental concern due to the polymer's widespread application, pronounced crystallinity, and intrinsic resistance to biodegradation. Although certain wild-type microorganisms demonstrate PET-hydrolyzing capabilities, their industrial applicability is constrained by slow proliferation, suboptimal catalytic performance, and limited resilience under environmental stress. These challenges highlight the imperative for engineered microbial platforms mediating robust, in situ PET depolymerization. This review discusses the emergence of genetically engineered <em>Escherichia coli</em> (<em>E. coli</em>) as a promising and versatile chassis for PET bioconversion. PETases and related hydrolases have been heterologously expressed and subjected to iterative protein engineering in <em>E. coli</em> to improve thermal stability, catalytic turnover rates, and substrate selectivity. In parallel, synthetic biology strategies have enabled the modular assembly of multi-enzyme cascades and surface display systems to enhance microbe–PET interfacial interactions and catalytic efficiency. Furthermore, integration of native and synthetic metabolic circuits within <em>E. coli</em> enables the biotransformation of ethylene glycol (EG) and terephthalic acid (TPA) into central metabolites, which are subsequently directed toward the biosynthesis of a diverse array of high-value bioproducts.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"85 ","pages":"Article 108713"},"PeriodicalIF":12.5,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145039087","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":"Modelling challenges to unlock the power of phototrophic systems for wastewater valorization","authors":"Francesca Casagli ,&nbsp;Andrea Turolla ,&nbsp;Damien J. Batstone ,&nbsp;Gabriel Capson-Tojo ,&nbsp;Elena Ficara ,&nbsp;Joan García ,&nbsp;Eva Gonzalez-Flo ,&nbsp;Julien Laurent ,&nbsp;Tatjana Lorenz ,&nbsp;Michaël Pierrelée ,&nbsp;Benedek Gy. Plósz ,&nbsp;Gustavo Henrique Ribero Da Silva ,&nbsp;Ángel Robles ,&nbsp;Simone Rossi ,&nbsp;Estel Rueda ,&nbsp;Lars Stegemüller ,&nbsp;Jean-Philippe Steyer ,&nbsp;Olivier Bernard ,&nbsp;Borja Valverde-Pérez","doi":"10.1016/j.biotechadv.2025.108709","DOIUrl":"10.1016/j.biotechadv.2025.108709","url":null,"abstract":"<div><div>Phototrophic microorganisms are gaining prominence for their dual role in wastewater treatment and resource recovery, converting wastewater into valuable bioproducts. However, their effective deployment needs robust modelling frameworks capable of predicting performance across complex, real-world scenarios. Despite significant advances, key challenges hinder the development and application of such models:<ul><li><span>●</span><span><div>Biological complexity: phototrophic systems involve intricate processes (e.g., photosynthesis, nutrient uptake, microbial interactions, and predation) that are difficult to represent accurately due to their dynamic interdependencies.</div></span></li><li><span>●</span><span><div>Environmental variability: permanent fluctuations in light, temperature, pH, and toxic compounds in outdoor reactors require high-resolution dynamic data for reliable model calibration and prediction.</div></span></li><li><span>●</span><span><div>Data limitations: lack of comprehensive, high-quality datasets (e.g., biological, environmental, and operational conditions) constrains model development, particularly for data-driven approaches.</div></span></li><li><span>●</span><span><div>Multi-scale integration: bridging molecular, cellular, and ecosystem-level processes into a unified modelling framework, including physics, remains a significant hurdle.</div></span></li><li><span>●</span><span><div>Parameter and uncertainty management: models often suffer from non-identifiable parameters, sensitivity to approximations, and insufficient validation against long-term experimental data.</div></span></li><li><span>●</span><span><div>Balancing complexity and applicability: selecting the appropriate level of ecological and mathematical details, tailored to specific applications (e.g., biomass production and nutrient removal) and data availability is critical yet challenging.</div></span></li><li><span>●</span><span><div>Computational and interdisciplinary barriers: high computational costs, especially for hybrid and data-driven models, alongside the need for cross-disciplinary collaboration, further complicate model development.</div></span></li><li><span>●</span><span><div>To overcome these barriers, this work argues for standardized protocols in model design, calibration and validation, alongside enhanced data collection and reconciliation efforts. Integrating innovative approaches, such as metabolic modelling, machine learning and hybrid modelling into digital twins, will be essential to unlock the full potential of phototrophic systems, bridging the gap between theoretical models and industrial implementation.</div></span></li></ul></div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"85 ","pages":"Article 108709"},"PeriodicalIF":12.5,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032653","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":"Electro-interactions: A review of the effects of electric fields on bacterial cells","authors":"Panagiota Dima,&nbsp;Ioannis S. Chronakis,&nbsp;Ana C. Mendes","doi":"10.1016/j.biotechadv.2025.108711","DOIUrl":"10.1016/j.biotechadv.2025.108711","url":null,"abstract":"<div><div>Electric fields significantly influence bacterial cells by altering their physiology, membrane properties, membrane potential, and permeability, as well as their metabolism and mobility. These interactions result in observable changes in growth rates, cellular morphology, and gene expression. This review provides a comprehensive examination of the effects of electric fields on bacterial cells, focusing specifically on mechanisms such as electro-stimulation, electroporation, electrophoresis, and dielectrophoresis. Examples of such effects include increasing bacterial proliferation rates, enhancing the production of valuable compounds, and influencing cell movement, orientation, and aggregation. The review highlights how these mechanisms can be employed to customize bacterial properties for targeted outcomes. Applications across various sectors are also discussed, such as using electric fields to improve fermentation efficiency in the food and biotechnology industry, to extend cell stability and viability, and to precisely control cell adhesion or detachment from surfaces, benefiting both biotechnology and pharmaceutical fields. Furthermore, this review paper emphasizes the importance of ongoing research to fully unlock the potential of electric fields in both scientific research and industrial applications involving bacteria.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"85 ","pages":"Article 108711"},"PeriodicalIF":12.5,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032643","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 nanopore direct RNA sequencing and its impact on biological research","authors":"Kai Sun ,&nbsp;Jiaxin Li ,&nbsp;Chaohao Chen ,&nbsp;Xin Zhou ,&nbsp;Guofang Ma ,&nbsp;Lingfeng Mao ,&nbsp;Qiao Tang ,&nbsp;Biao Ma ,&nbsp;Dong Li ,&nbsp;Zhijuan Chen ,&nbsp;Congnan Cen ,&nbsp;Xuping Shentu ,&nbsp;Zihong Ye ,&nbsp;Xiaoping Yu","doi":"10.1016/j.biotechadv.2025.108710","DOIUrl":"10.1016/j.biotechadv.2025.108710","url":null,"abstract":"<div><div>Nanopore direct RNA sequencing (DRS) is a transformative technology that enables full-length, single-molecule sequencing of native RNA, capturing transcript isoforms and preserving epitranscriptomic modifications without cDNA conversion. This review outlines key advances in DRS, including optimized protocols for mRNA, rRNA, tRNA, circRNA, and viral RNA, as well as analytical tools for isoform quantification, poly(A) tail measurement, fusion transcript identification, and base modification profiling. We highlight how DRS has redefined transcriptomic studies across diverse systems—from uncovering novel transcripts and alternative splicing events in cancer, plants, and parasites to enabling the direct detection of m6A, m5C, pseudouridine, and RNA editing events. Emerging applications such as co-transcriptional splicing analysis, lncRNA and circRNA discovery, and real-time RNA structural mapping are also discussed. Beyond basic research, DRS offers powerful capabilities in mRNA vaccine quality control and RNA-based data storage. Despite current limitations in sequencing accuracy, input requirements, and cost, ongoing improvements in nanopore chemistry, basecalling algorithms, and machine learning integration are rapidly expanding DRS utility. As it matures, DRS is poised to become a core platform for high-resolution transcriptome profiling, RNA regulatory analysis, and integrative multi-omics applications, offering novel insights into gene expression, regulation, and evolution.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"85 ","pages":"Article 108710"},"PeriodicalIF":12.5,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145027275","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":"Intersecting precision fermentation for global cell-based food production innovation: Challenges and opportunities","authors":"Fuqing Gao ,&nbsp;Shaoran Shi ,&nbsp;Yang Zhao ,&nbsp;Dong Yang ,&nbsp;Xiaojun Liao","doi":"10.1016/j.biotechadv.2025.108712","DOIUrl":"10.1016/j.biotechadv.2025.108712","url":null,"abstract":"<div><div>Precision fermentation represents an innovative cell-based production approach that employs synthetic biology and metabolic engineering tools, revolutionizing global food production by utilizing “microbial cell factories” to produce added-value ingredients. However, its global implementation is hindered by technological and scalability bottlenecks, regulatory fragmentation, regional accessibility and consumer acceptance, and nutritional trade-offs challenges. This review utilizes illustrated case studies and modeling analysis to present a detailed exploration of precision fermentation intersecting with global cell-based food production, discussing actionable research gaps and insights as well as advanced bioengineering practices and analytical techniques, to address these challenges for ongoing academic research, industrial applications and policy initiatives, thus supporting the transition of fermentation-enabled food production toward efficient and sustainable manufacturing. Moreover, attention is also dedicated to ethical concerns such as intellectual property monopolies and equitable technology access in low-resource regions. We highlighted crucial elements such as synthetic biology and metabolic engineering tools with advancements in precision nutrition, recognizing their crucial roles in large-scale fermentation-enabled production, market adoption, and elaborating on the “hidden hunger” hypotheses regarding the mechanism of potential “Nutritional starvation” risk and proposing mitigation strategies. Adopting computer-aided engineering (CAE), artificial intelligence (AI), and automation to refine fermentation processes presents promising avenues for enhancing production efficiency and sustainability, while the limitations of these tools and research priorities are also discussed. We further propose a visionary framework where upcoming food innovations meet consumer expectations for health and environmental responsibility, ultimately propelling the field of fermented food into a new era of technological sophistication and societal impact.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"85 ","pages":"Article 108712"},"PeriodicalIF":12.5,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032682","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":"Engineered microbial production of carotenoids and their cleavage products: Recent advances and prospects","authors":"Ping Lin ,&nbsp;Guocheng Du ,&nbsp;Jian Chen ,&nbsp;Juan Zhang ,&nbsp;Zheng Peng","doi":"10.1016/j.biotechadv.2025.108708","DOIUrl":"10.1016/j.biotechadv.2025.108708","url":null,"abstract":"<div><div>Carotenoids and their cleavage products (referred to as apocarotenoids) have functional properties such as antioxidant activity, fragrance, and color that are important in the pharmaceutical, healthcare, cosmetics, and food industries. Currently, carotenoids and apocarotenoids are primarily obtained through extraction from natural sources or chemical synthesis, both of which are associated with inefficiencies, environmental impact, and product limitations. Ongoing advances in metabolic engineering and synthetic biology have positioned heterologous biosynthesis as a promising, efficient, and sustainable production strategy. This review summarizes recent progress in carotenoid and apocarotenoid biosynthesis, detailing the key biosynthetic pathways originating from mevalonate and methylerythritol phosphate, with a focus on the enzymes involved in carotenoid cleavage. We also highlight significant advancements in microbial production, emphasizing various metabolic engineering strategies aimed at enhancing microbial production efficiency. Lastly, we discuss potential future research directions for the biosynthesis of these compounds.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"85 ","pages":"Article 108708"},"PeriodicalIF":12.5,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022752","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}