Biotechnology advances最新文献

{"title":"Brews, fuels, and opioids: Expanding the yeast Ehrlich pathway for chemical and pharmaceutical manufacturing.","authors":"Anastasia E C Rumpl, Joshua R Goodhew, Paul F Kelly, Mika Hirano, Michael E Pyne","doi":"10.1016/j.biotechadv.2025.108684","DOIUrl":"10.1016/j.biotechadv.2025.108684","url":null,"abstract":"<p><p>The Ehrlich pathway is a catabolic process that imparts Saccharomyces cerevisiae and other yeasts with the ability to utilize branched-chain and aromatic amino acids as a source of nitrogen. Using this route, amino acids are transaminated to α-keto acids and the liberated ammonia is utilized for assimilatory reactions. This process leaves behind an array of aliphatic and aromatic carbon skeletons (fusel metabolites) that have found a multitude of uses in the production of flavors, chemicals, and pharmaceuticals. This review provides an update on the genetics and biochemistry of the Ehrlich pathway with an emphasis on the biotechnological valorization of fusel metabolites. We outline the impact of fusel metabolism on the organoleptic properties of fermented beverages and recap ongoing efforts to repurpose the Ehrlich pathway for production of advanced biofuels. We also highlight recent activity directed at producing opioids and other plant benzylisoquinolines, as well as engineering new-to-nature alkaloids by rewiring the yeast Ehrlich pathway. Collectively, these efforts have stimulated a deeper understanding of yeast fusel metabolism and opened new opportunities for biomanufacturing using conventional and non-conventional yeasts.</p>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":" ","pages":"108684"},"PeriodicalIF":12.5,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803324","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":"Bacillus spore germination: Interpretation of the spore germination mechanism and innovation of the inactivation strategies.","authors":"Yangfu Li, Juan Wang, Guicheng Zhou, Xiaoming Yuan, Ling Chen, Qihui Gu, Youxiong Zhang, Xianhu Wei, Yu Ding, Qingping Wu","doi":"10.1016/j.biotechadv.2025.108683","DOIUrl":"10.1016/j.biotechadv.2025.108683","url":null,"abstract":"<p><p>Bacillus is a ubiquitous genus renowned for its ability to form highly resilient spores, posing significant challenges to the food industry. As society progresses, the demand for high-quality food continues to rise. While reducing excessive processing helps maintain nutritional value and quality which fits the demands from consumers, it increases the risk of spore contamination. Germination-inactivation strategies offer a promising solution by converting spores into vegetative cells, which can be eliminated through milder treatments, thus preserving food quality while ensuring food safety. However, the limited efficiency of current methods to induce germination, particularly due to the emergence of super-dormant spores, hinders their widespread application. Optimizing spore germination is critical for the successful implementation of the germination-inactivation strategies. This study aims to provide a comprehensive overview of the mechanisms underlying Bacillus spore germination, focusing on the latest advances in signal transduction and macromolecular biosynthesis. Additionally, we systematically summarize the characteristics of super-dormant spores and their potential causes. Current methods for enhancing spore germination efficiency are thoroughly reviewed, and their limitations are discussed in detail. Based on these insights, innovative solutions are proposed to address the existing challenges. Recent research has unveiled the signal transduction mechanisms involved in spore germination, emphasizing the critical role of ion release. Moreover, transcription and translation likely govern dipicolinic acid release and cortex hydrolysis, respectively, with spores being able to rapidly initiate transcription through pre-located RNA polymerase. Interestingly, the emergence of super-dormant spores is influenced by both permanent and transient factors. To improve spore germination efficiency, promising solutions include innovative screening of germinants, optimization of the key factors of thermal activation and pressure-induced germination, and utilization of key substances during germination process.</p>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":" ","pages":"108683"},"PeriodicalIF":12.5,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803368","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":"Dissecting the specificity of sugar code recognition - Unleashing the biomedical potential of galectins by protein engineering.","authors":"Marta Kalka, Julia Ptak, Paulina Gregorczyk, Krzysztof Ciura, Aleksandra Chorążewska, Subhradeep Haldar, Natalia Porębska, Ewa Marcinkowska, Łukasz Opaliński","doi":"10.1016/j.biotechadv.2025.108681","DOIUrl":"10.1016/j.biotechadv.2025.108681","url":null,"abstract":"<p><p>The cell surface is extremely rich in multilayered information that exists in the form of complex monosaccharide assemblies, establishing a cellular sugar code. The sugar code is specifically deciphered by extracellular lectins, galectins, which are capable of recognizing sugar code components and transforming the code into precise cellular activities. Galectin-dependent reading of the sugar code relies on two major features: the specific recognition of sugars by the galectins' carbohydrate recognition domains (CRDs) and the modular architecture of galectins or their oligomerization. These two characteristics of galectins are essential for most of galectins' functions, as they ensure the specificity of sugar code recognition and permit multivalent interactions with carbohydrate ligands. The natural galectins are characterized by relatively fixed modular architecture, which allows for evolutionarily defined reading of the sugar code, limiting the spectrum of biological activities of galectins. Distinct protein engineering approaches, like linker modulation, crosslinking, domain swapping or fusion with oligomerization scaffolds allow for the modulation of galectin multivalency in order to overcome the natural decoding limitations of galectins and permit alternative reading of the sugar code. In this review, we we provide an overview of the architectures of engineered galectins with altered valency and discuss how alternative reading of the code by such proteins may prove beneficial in biotechnology.</p>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":" ","pages":"108681"},"PeriodicalIF":12.5,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144798076","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, Shuting Geng, Jianqiu Yu, Leilei Lu, Yanhua Liu, Jianqiu Chen, Qianjiahua Liao, Ruixin Guo","doi":"10.1016/j.biotechadv.2025.108733","DOIUrl":"https://doi.org/10.1016/j.biotechadv.2025.108733","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":" ","pages":"108733"},"PeriodicalIF":12.5,"publicationDate":"2025-10-06","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":"Environments contaminated by pesticides are hotspots for the selection of bacterial chassis for biotechnological applications.","authors":"Caroline Rosa Silva, Marcos Pileggi","doi":"10.1016/j.biotechadv.2025.108723","DOIUrl":"10.1016/j.biotechadv.2025.108723","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":" ","pages":"108723"},"PeriodicalIF":12.5,"publicationDate":"2025-10-03","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":"Synthetic biology for scalable production of medical polyhydroxyalkanoates: Advances and applications.","authors":"Yong Chen, Zheng-Dong Qi, Rui Ji, Na Shi, Huayou Chen, Dai-Xu Wei","doi":"10.1016/j.biotechadv.2025.108722","DOIUrl":"https://doi.org/10.1016/j.biotechadv.2025.108722","url":null,"abstract":"<p><p>Polyhydroxyalkanoates (PHAs), characterized by their biodegradability and biocompatibility, present a promising, sustainable alternative to conventional synthetic polymers for biomedical applications. This study highlights the diversity of PHA monomers and structures, controllable biodegradability, and excellent biocompatibility, emphasizing their suitability for tissue engineering (bone, skin, cardiovascular, oral), anti-hair loss treatments, and drug delivery systems. Significant advancements in synthetic biology, encompassing CRISPR/Cas genome editing, promoter engineering, ribosome binding site optimization, metabolic pathway fine-tuning, and morphology engineering, have led to substantial improvements in PHA production efficiency and a reduction in associated costs. The adoption of next-generation industrial biotechnology (NGIB) using halophiles further enhances economic viability and simplifies the production process. The current commercial landscape and the future prospects of medical-grade PHAs, poised to become mainstream biodegradable materials, are also critically discussed.</p>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":" ","pages":"108722"},"PeriodicalIF":12.5,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145231610","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, Barry Trimmer, David L Kaplan","doi":"10.1016/j.biotechadv.2025.108721","DOIUrl":"10.1016/j.biotechadv.2025.108721","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":" ","pages":"108721"},"PeriodicalIF":12.5,"publicationDate":"2025-10-01","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":"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":"2025-09-30","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":"A comprehensive review of methodological and technological advancement in PCR during the last 15 years","authors":"Zhenqing Li ,&nbsp;Xingyu Yang ,&nbsp;Bo Yang ,&nbsp;Jing Yang ,&nbsp;Chunxian Tao ,&nbsp;Dawei Zhang ,&nbsp;Yoshinori Yamaguchi","doi":"10.1016/j.biotechadv.2025.108719","DOIUrl":"10.1016/j.biotechadv.2025.108719","url":null,"abstract":"<div><div>Polymerase chain reaction (PCR) has evolved from a foundational DNA amplification tool to a sophisticated analytical platform driving precision medicine. This review highlights PCR from fundamental principles to advanced techniques and diverse applications. It summarized the development of PCR technologies including nested PCR, quantitative PCR, multiplex PCR, and various kinds of microfluidic PCR (e.g., convective PCR and continuous flow PCR) that collectively enhanced sensitivity from micrograms to single molecules. Advancements in technology have propelled the application of PCR in two key directions: (1) integration with microfluidic chips for point-of-care testing (POCT), and (2) the shift from qualitative to absolute quantification, enabling the detection of single DNA molecules and thereby advancing the field of precision medicine. Furthermore, we discussed the application of machine vision and neural networks in digital PCR systems significantly enhanced the accuracy of positive microchamber identification in chip-based analyses.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"85 ","pages":"Article 108719"},"PeriodicalIF":12.5,"publicationDate":"2025-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190660","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 transport systems of organic sulfur compounds: Diversity and implications for biocatalysis, healthcare, and environmental biotechnology","authors":"Fakhra Liaqat ,&nbsp;Mahammed Ilyas Khazi ,&nbsp;Wael Ismail","doi":"10.1016/j.biotechadv.2025.108718","DOIUrl":"10.1016/j.biotechadv.2025.108718","url":null,"abstract":"<div><div>The global sulfur cycle plays a vital role in human health, global warming, and biogeochemistry. Organic sulfur compounds constitute a substantial sulfur reservoir and serve as an energy and/or carbon source for prokaryotes. In addition, microbial interactions with organic sulfur compounds are pivotal for several biotechnological applications in petroleum biorefining, industrial biocatalysis, bioremediation, healthcare, and plant growth promotion. Microbial degradation of organic sulfur compounds is hindered by slow degradation rates, substrate specificity, toxicity of by-products, and challenges in scalability and efficiency. While degradation pathways of some organic sulfur compounds have been elucidated, transport systems involved in their uptake and efflux remain less explored. Regulating the uptake and efflux of organic sulfur compounds in microorganisms can help overcome several of the limitations associated with their transformation. Membrane transporters are not only crucial for the uptake and efflux of organic sulfur compounds but also play a key role in stress tolerance by facilitating the excretion of toxic metabolites. Understanding the intricacies of these transporters provides valuable insights into microbial ecology and the development of strategies for harnessing microbial sulfur metabolism for important biotechnological applications. This review systematically presents the diversity, mechanisms, and potential evolution pathways of microbial membrane transporters involved in organic sulfur compounds acquisition. Furthermore, it highlights and discusses advances in the characterization of transporter systems and current limitations in using transporter systems for fuel biodesulfurization and organic sulfur compound degradation. Eventually, we explore the implications of organic sulfur compounds transporters in biotechnology and identify future research directions toward leveraging the biotechnological potential of microbial sulfur metabolism, fueled by advanced techniques of systems microbiology, metabolic engineering, as well as artificial intelligence.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"86 ","pages":"Article 108718"},"PeriodicalIF":12.5,"publicationDate":"2025-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145130051","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}