Bei Ouyang , Guoping Wang , Ziyan Hu , Qiling Liu , Wenwen Zhao , Xihua Zhao
{"title":"A novel directed evolution approach for co-evolution of β-glucosidase activity and organic acid tolerance","authors":"Bei Ouyang , Guoping Wang , Ziyan Hu , Qiling Liu , Wenwen Zhao , Xihua Zhao","doi":"10.1016/j.jbiotec.2025.02.009","DOIUrl":"10.1016/j.jbiotec.2025.02.009","url":null,"abstract":"<div><div>Directed evolution is a potent tool for protein engineering; however, Error-prone PCR and DNA Shuffling often lead to a high frequency of negative and reverse mutations, especially in the case of large genes. This study introduces two innovative techniques to tackle these challenges: Segmental error-prone PCR (SEP) and Directed DNA shuffling (DDS). SEP involves averagely dividing large genes into small fragments, independently and randomly mutagenizing them in vitro, and reassembling them as well as other unmutated fragments in <em>Saccharomyces cerevisiae</em>. DDS selectively amplifies mutated fragments of positive variants from SEP and reassembles them in <em>S. cerevisiae</em> to produce complete genes with cumulative positive mutations. We have used these two techniques to simultaneously improve the activity of β-glucosidase and its tolerance to organic acids, which validates the effectiveness and feasibility of the approach.</div></div>","PeriodicalId":15153,"journal":{"name":"Journal of biotechnology","volume":"401 ","pages":"Pages 1-10"},"PeriodicalIF":4.1,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143464468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sung-Hyuk Han , Seo-Young Park , Hyun-Myoung Cha , Kwang-Bae Lee , Jin-Hyuk Lim , Dong-Yup Lee
{"title":"A robust scale-down model development and process characterization for monoclonal antibody biomanufacturing using multivariate data analysis","authors":"Sung-Hyuk Han , Seo-Young Park , Hyun-Myoung Cha , Kwang-Bae Lee , Jin-Hyuk Lim , Dong-Yup Lee","doi":"10.1016/j.jbiotec.2025.02.007","DOIUrl":"10.1016/j.jbiotec.2025.02.007","url":null,"abstract":"<div><div>Quality by Design (QbD) principles are extensively applied in biopharmaceutical manufacturing processes to ensure the consistent production of high-quality biotherapeutic products through achieving a deeper understanding of critical process parameters (CPPs), critical quality attributes (CQAs), and their interrelationships as well as establishing appropriate process control strategies. To do so, herein, we involve utilizing advanced multivariate data analysis (MVDA) in the context of scale-down model (SDM) development and validation as an ingenious approach for enhancing process efficiency and achieving greater regulatory compliance in the biomanufacturing of biologics. First, MVDA was applied to develop and evaluate several SDMs under various production conditions, including changes in scale-dependent parameters. This allowed the establishment of a practical SDM that closely approximated the process performance of manufacturing-scale batches. Furthermore, this approach enabled the identification not only of potential CPPs but also specific performance attributes such as ammonia, that had a significant impact on the CQAs. Moreover, it was deduced that the N-1 seed culture represents a critical process step influencing both quality and performance attributes in the upstream process from these approaches. This deduction was subsequently confirmed through experimental validation. Our findings offer valuable insights into streamlining the development of upstream biologics, particularly in terms of process characterization, thereby suggesting strategies for time and cost savings.</div></div>","PeriodicalId":15153,"journal":{"name":"Journal of biotechnology","volume":"401 ","pages":"Pages 11-20"},"PeriodicalIF":4.1,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143464469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bakr Ahmed Taha , Ali J. Addie , Surjeet Chahal , Adawiya J. Haider , Sarvesh Rustagi , Norhana Arsad , Vishal Chaudhary
{"title":"Unlocking new frontiers in healthcare: The impact of nano-optical biosensors on personalized medical diagnostics","authors":"Bakr Ahmed Taha , Ali J. Addie , Surjeet Chahal , Adawiya J. Haider , Sarvesh Rustagi , Norhana Arsad , Vishal Chaudhary","doi":"10.1016/j.jbiotec.2025.02.005","DOIUrl":"10.1016/j.jbiotec.2025.02.005","url":null,"abstract":"<div><div>Nano-optical biosensors have emerged as transformative tools in healthcare and clinical research, offering rapid, portable, and specific diagnostic solutions. This review critically analyzes the recent advancements, translational challenges, and sustainable approaches in nano-optical biosensor implementation for biomedical applications. We explore the integration of innovative nanomaterials, microelectronics, and molecular biology techniques that have significantly enhanced biosensor sensitivity and specificity, enabling detection of biomarkers ranging from cancer indicators to cardiovascular markers. The potential of nanoplasmonic and silicon photonic biosensors in overcoming current limitations is discussed, alongside the promising integration of artificial intelligence and Internet of Things technologies for improved data analytics and clinical validation. We address key challenges, including size constraints, energy efficiency, and integration with existing technologies, and propose sustainable strategies for eco-friendly materials, energy-efficient designs, and circular economy approaches. The review also examines emerging trends such as multiplexed sensing platforms, wearable biosensors, and their applications in personalized medicine. By critically assessing these developments, we provide insights into the prospects of nano-optical biosensors and their potential to revolutionize point-of-care diagnostics and personalized healthcare, while emphasizing the need for interdisciplinary collaboration to overcome remaining obstacles in translating these technologies from laboratory research to real-world clinical applications.</div></div>","PeriodicalId":15153,"journal":{"name":"Journal of biotechnology","volume":"400 ","pages":"Pages 29-47"},"PeriodicalIF":4.1,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143427774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Waste cooking oils as a sustainable feedstock for bio-based application: A systematic review","authors":"Antonio Caporusso , Matteo Radice , Antonino Biundo , Ruggiero Gorgoglione , Gennaro Agrimi , Isabella Pisano","doi":"10.1016/j.jbiotec.2025.02.003","DOIUrl":"10.1016/j.jbiotec.2025.02.003","url":null,"abstract":"<div><div>Waste cooking oils (WCOs) are common wastes and promising green, eco-friendly and sustainable feedstocks for bio-based applications. While the primary valorisation strategy revolves around the concept of waste-to energy, new research trends have emerged in the last decade. This systematic review provides a comprehensive analysis of the current state of the art in the conversion of WCOs into bio-based molecules. Based on the PRISMA methodology, 64 papers were selected using different databases and sources, such as: PubMed, ScienceDirect, Scopus and MDPI. The data extraction process focused on studies reporting the biological and chemical conversion of WCOs into value-added bioproducts. Many of the selected publications deal with the development of bioactive molecules, including biosurfactants, with application in pharmaceuticals, food, cosmetics, and bioremediation. Bioconversion processes mainly featured engineered <em>Yarrowia lipolytica</em> and <em>Escherichia coli</em> strains, even if additional microorganisms were also employed. In the same way, different chemical processes have been thoroughly studied. A smaller segment of research is directed to the production of feed supplements and soaps. Regulatory constraints limit further development in feed supplements due to potential contaminants, while soap production needs further stability studies. The present systematic review shows promising outcomes in the valorisation of WCOs through the development of value-added molecules and products. Despite the wide range of applications, these findings identify that the scalability and economic sustainability of the selected processes require further investigation. This study seeks to summarize the current state of the art and identify potential gaps to advance the industrialization of WCOs valorisation.</div></div>","PeriodicalId":15153,"journal":{"name":"Journal of biotechnology","volume":"400 ","pages":"Pages 48-65"},"PeriodicalIF":4.1,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143425341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiaona Chen , Jianjian Tong , Kai Chen , Ruiqi Ma , Zhen Gao , Yan Li , Honghua Jia
{"title":"Identification of a sucrose phosphorylase variant from Streptococcus mutans for production of epigallocatechin gallate glucosides","authors":"Xiaona Chen , Jianjian Tong , Kai Chen , Ruiqi Ma , Zhen Gao , Yan Li , Honghua Jia","doi":"10.1016/j.jbiotec.2025.02.004","DOIUrl":"10.1016/j.jbiotec.2025.02.004","url":null,"abstract":"<div><div>Epigallocatechin gallate (EGCG) primarily extracted from green tea, exhibits significant antioxidant, hypolipidemic, and anticancer properties. Nevertheless, the limited aqueous solubility and bioavailability of EGCG impede its practical applications. Glycosylation modification of EGCG is an effective method for enhancing its properties. In the present study, a thermally stable variant of sucrose phosphorylase from <em>Streptococcus mutans</em> (<em>Sm</em>SP) was identified as having catalytic activity for glycosylation of EGCG. The optimal temperature and pH for <em>Sm</em>SP were determined to be 45°C and 6, respectively. The mono-glycosylation product of EGCG was structurally characterized as (−)-epigallocatechin gallate 4′-O-α-D-glucopyranoside. Under optimal reaction conditions (8 % methanol, 10 g/L EGCG, 300 g/L sucrose, 40 U/mL crude enzyme, 35°C, and 24 h), the conversion rate of EGCG reached 80.79 %. Hydrogen bonding interactions between the enzyme and ligands may enhance the stability and catalytic activity of <em>Sm</em>SP. Two active site loops significantly influence the selective formation of EGCG glycosides. These insights expand our understanding of the structural basis of sucrose phosphorylases in the synthesis of EGCG glycosides.</div></div>","PeriodicalId":15153,"journal":{"name":"Journal of biotechnology","volume":"401 ","pages":"Pages 21-31"},"PeriodicalIF":4.1,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143414394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Facundo Muñiz-Paredes , Olena P. Ishchuk , Dina Petranovic
{"title":"Impact of liquid and solid-state cultures on hemoglobin production and oxidative state in Saccharomyces cerevisiae","authors":"Facundo Muñiz-Paredes , Olena P. Ishchuk , Dina Petranovic","doi":"10.1016/j.jbiotec.2025.01.020","DOIUrl":"10.1016/j.jbiotec.2025.01.020","url":null,"abstract":"<div><div>Recombinant human hemoglobin gained attention due to its potential use as a blood-free oxygen carrier substitute. To enhance human hemoglobin production in <em>Saccharomyces cerevisiae</em>, various genetic engineering strategies have been employed, including: increasing intracellular heme levels, minimizing heme and protein degradation pathways, and co-expressing the α-hemoglobin stabilizing protein (AHSP). Solid-state culture (SSC) may enhance hemoglobin production by increasing heme biosynthesis, as it relates to intracellular oxygen availability. A comparative analysis of heme and hemoglobin production was conducted between liquid culture (LC) and SSC using the <em>S. cerevisiae</em> AHSP strain. While both systems exhibited comparable heme and hemoglobin yields per cell, a significant 18 % increase in biomass was observed in SSC. The expression of the aerobic master gene <em>HAP1</em> remained consistent between both systems, however, <em>CYC1</em> (regulated by <em>HAP1</em>) was two-fold overexpressed in SSC, indicating higher oxygen transference and possibly more efficient electron transport. Several antioxidant genes were downregulated in the SSC, suggesting that LC may be more susceptible to electron leakage during oxidative phosphorylation, potentially due to the lower expression of <em>CYC1</em>. It is proposed that high expression of antioxidant genes in LC inhibits biomass production due to the metabolic burden of maintaining redox homeostasis. These differences between LC and SSC may explain the suitability of SSC as a platform for recombinant protein production.</div></div>","PeriodicalId":15153,"journal":{"name":"Journal of biotechnology","volume":"400 ","pages":"Pages 1-7"},"PeriodicalIF":4.1,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143391005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Progress on production of malic acid and succinic acid by industrially-important engineered microorganisms","authors":"Na Wu , Wenxin Wang , Jianguo Zhu","doi":"10.1016/j.jbiotec.2025.02.001","DOIUrl":"10.1016/j.jbiotec.2025.02.001","url":null,"abstract":"<div><div>Organic acids are widely used as additives in the food, pharmaceutical, chemical, and plastic industries. Currently, the industrial production methods of organic acids mainly include plant extraction and chemical synthesis. The latter mainly uses petroleum-based compounds as raw materials to synthesize organic acids through a series of chemical reactions. All of these methods have problems such as environmental pollution, high cost, and unsustainability. By contrast, microbial fermentation can effectively utilize a variety of carbon sources. Due to its low production cost, environmental friendliness, and high product purity, microbial fermentation has received increasing attention in recent years. However, the low yield and long fermentation cycle of microbial fermentation limits its industrial application. With the development of genomics, transcriptomics, and other omics technologies, the metabolic pathways of various strains producing organic acids have gradually been elucidated. Based on this, new technologies such as synthetic biology and high-throughput screening have also been extensively studied. This review summarizes the latest research progress in improving organic acid biosynthesis through metabolic engineering, focusing on L-malic acid (L-MA) and succinic acid (SA). Finally, we also discuss the challenges and future prospects of this field. This review has important reference value in the fields of food, pharmaceuticals, and chemicals, providing a theoretical basis for the study of organic acid biosynthesis.</div></div>","PeriodicalId":15153,"journal":{"name":"Journal of biotechnology","volume":"400 ","pages":"Pages 8-19"},"PeriodicalIF":4.1,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143382432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wenjie Zhao , Xianbo Su , Weizhong Zhao , Peipei Yan , Yixuan Zhou
{"title":"Experimental study on the mechanism of biological hydrogen sulfide generation from organic sulfur-rich coal","authors":"Wenjie Zhao , Xianbo Su , Weizhong Zhao , Peipei Yan , Yixuan Zhou","doi":"10.1016/j.jbiotec.2025.02.002","DOIUrl":"10.1016/j.jbiotec.2025.02.002","url":null,"abstract":"<div><div>Whether of primary or secondary origin, the presence of hydrogen sulfide (H<sub>2</sub>S) in coalbed methane (CBM) is commonly attributed to sulfate reduction facilitated by sulfate-reducing bacteria (SRB). However, the sulfate content in high-sulfur coal is exceptionally low, insufficient to function as a substrate for sulfate-reducing bacteria (SRB). In this study, an anaerobic digestion experiment was conducted with high-organic-sulfur coal collected from the Late Permian Longtan Formation in Guangxi Province as both the carbon and sulfur sources. The formation mechanism of H<sub>2</sub>S is revealed from the evolution rules of gas components, liquid organic matter, and microbial communities during the anaerobic digestion process. The findings indicate three distinct mechanisms contributing to the biological formation of H<sub>2</sub>S in coal seams: firstly, the degradation of readily degradable organic sulfur in coal by microorganisms possessing denitrification capabilities, primarily attributed to the activity of the <em>Wolinella</em>; secondly, The synergistic consortium involving SRB, Pseudomonas spp., and denitrifying Thiobacillus species mediates SO<sub>4</sub><sup>2-</sup> reduction and H₂S biogenesis through cross-metabolic interactions; thirdly, Methylotrophic methanogens employ the methyl groups of organic sulfides to produce CH<sub>4</sub> and H<sub>2</sub>S simultaneously. Therefore, biological H<sub>2</sub>S can be generated under the presence of a sulfur source, appropriate temperature, and conducive environmental conditions. This comprehension will contribute valuable insights to the discourse on the generation and enrichment patterns of H<sub>2</sub>S in natural coalbed methane. Additionally, it can offer practical avenues for the prevention and control of H<sub>2</sub>S through technological approaches.</div></div>","PeriodicalId":15153,"journal":{"name":"Journal of biotechnology","volume":"400 ","pages":"Pages 20-28"},"PeriodicalIF":4.1,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Efficient production of spermidine from Bacillus amyloliquefaciens by enhancing synthesis pathway, blocking degradation pathway and increasing precursor supply","authors":"Ziyue Zhao, Ailing Guo, Dian Zou, Zhou Li, Xuetuan Wei","doi":"10.1016/j.jbiotec.2024.12.001","DOIUrl":"10.1016/j.jbiotec.2024.12.001","url":null,"abstract":"<div><div>Spermidine has broad application potential in food, medicine and other fields. In this study, a novel <em>Bacillus amyloliquefaciens</em> cell factory was constructed for production of spermidine from renewable<!--> <!-->biomass resources. Firstly, the <em>speB</em> gene was found to be optimal for synthesis of spermidine, and the function of SpeB was explained by amino acid sequence analysis and molecular docking. By replacing the native promoter of the <em>speEB</em> operon with the P43, the synthesis of spermidine was significantly enhanced in <em>B. amyloliquefaciens</em> HSPM1-P43<em>speEB</em>. After knockout of the genes <em>yobN</em> and <em>bltD</em> associated with spermidine degradation, the spermidine titer of the strain HSPM2 was further improved to 115.96 mg/L, increased by 108 % compared to HSPM1-P43<em>speEB</em>. Subsequently, the titer of spermidine was further increased to 277.47 mg/L through enhancing the supply of the precursor methionine by overexpression of <em>speD</em>. Finally, the renewable biomass resources, xylose and feather meal were optimized to produce spermidine, and the maximum titer is up to 588.10 mg/L after optimization. In conclusion, an efficient spermidine producing <em>B. amyloliquefaciens</em> was constructed through combinatorial metabolic engineering strategies, and the sustainable production of spermidine was achieved using the biomass resources of xylose and feather meal.</div></div>","PeriodicalId":15153,"journal":{"name":"Journal of biotechnology","volume":"398 ","pages":"Pages 87-96"},"PeriodicalIF":4.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A review towards sustainable analyte detection: Biomimetic inspiration in biosensor technology","authors":"Pratistha Bhagat , Lata Sheo Bachan Upadhyay","doi":"10.1016/j.jbiotec.2024.11.015","DOIUrl":"10.1016/j.jbiotec.2024.11.015","url":null,"abstract":"<div><div>The branch of biomimetics has witnessed a profound impact on the field of biosensor technology, reflected in sustainable analyte detection. A vast array of biosensor platforms with improved/upgraded performance have been developed and reported. No wonder the motivation from the field of biomimetics has a huge impact on generating detection systems with escalated degrees of manipulation and tunability at different levels. More recently, biomimetic biosensor technology has found potential in constructing bio-inspired materials such as aptamers, MIPs, nanozymes, DNAzymes, Synzymes, etc. to be integrated with biosensor fabrication. The establishment of a sensing setup is not limited to the bioreceptor fabrication; the construction of transducing element using biomimetic material have been reported too. Moreover, to serve a biosensing of target analyte from a fatal diseased sample different biomimetic architectures can be designed that mimic in-vivo microenvironmental surroundings to get an exact microenvironment equivalent to natural conditions leading towards designing of a precise treatment strategy. This research area is ever-evolving as there is a scope for upgradation and refinement due to advancing technologies including nanotechnology, biomimetic nanomaterials, microfluidics, optical sensors, etc. This review is an attempt to comprehend and juxtapose the very primary innovations in the field of biomimetic biosensor technology to realize its comprehensive and wide-range scope and possibilities.</div></div>","PeriodicalId":15153,"journal":{"name":"Journal of biotechnology","volume":"398 ","pages":"Pages 51-65"},"PeriodicalIF":4.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}