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A Two-Step Process for Converting Methane to Canthaxanthin Using Methylococcus capsulatus (Bath) Biomass and Engineered Yarrowia lipolytica 利用荚膜甲基球菌(Bath)生物质和工程解脂耶氏菌将甲烷转化为角黄素的两步法研究
IF 3.2 3区 生物学
Biotechnology Journal Pub Date : 2025-06-09 DOI: 10.1002/biot.70043
Maria O. Taratynova, Ivan M. Tarasov, Iuliia M. Fedyaeva, Dmitry A. Dementev, Veronika A. Gorchakova, Margarita A. Tarasova, Alexander S. Fedorov, Tigran V. Yuzbashev, Sergey P. Sineoky, Evgeniya Y. Yuzbasheva
{"title":"A Two-Step Process for Converting Methane to Canthaxanthin Using Methylococcus capsulatus (Bath) Biomass and Engineered Yarrowia lipolytica","authors":"Maria O. Taratynova,&nbsp;Ivan M. Tarasov,&nbsp;Iuliia M. Fedyaeva,&nbsp;Dmitry A. Dementev,&nbsp;Veronika A. Gorchakova,&nbsp;Margarita A. Tarasova,&nbsp;Alexander S. Fedorov,&nbsp;Tigran V. Yuzbashev,&nbsp;Sergey P. Sineoky,&nbsp;Evgeniya Y. Yuzbasheva","doi":"10.1002/biot.70043","DOIUrl":"https://doi.org/10.1002/biot.70043","url":null,"abstract":"<div>\u0000 \u0000 <p>Methane biotransformation is gaining attention for the bio-industry and environmental protection. This study presents an approach for converting methane to canthaxanthin using <i>Methylococcus capsulatus</i> biomass and <i>Yarrowia lipolytica</i>. <i>Y. lipolytica</i> was engineered to introduce the canthaxanthin biosynthesis pathway, increase the acetyl-CoA flux, and boost hexose catabolism. In methanotroph-derived medium with molasses, canthaxanthin titer reached 1.2 g/L, advancing cost-effective, sustainable bioproduction.</p>\u0000 </div>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144244403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Simultaneous Repression of GLUCAN WATER DIKINASE 1 and STARCH BRANCHING ENZYME 1 in Potato Tubers Leads to Starch With Increased Amylose and Novel Industrial Properties 马铃薯块茎中葡聚糖水二激酶1和淀粉分支酶1的同时抑制导致淀粉直链淀粉增加和新的工业特性
IF 3.2 3区 生物学
Biotechnology Journal Pub Date : 2025-06-09 DOI: 10.1002/biot.70051
Muyiwa S. Adegbaju, Nina Gouws, Christell van der Vyver, Pedri Claassens, Jens Kossmann, Michaela Fischer-Stettler, Samuel C. Zeeman, James R. Lloyd
{"title":"Simultaneous Repression of GLUCAN WATER DIKINASE 1 and STARCH BRANCHING ENZYME 1 in Potato Tubers Leads to Starch With Increased Amylose and Novel Industrial Properties","authors":"Muyiwa S. Adegbaju,&nbsp;Nina Gouws,&nbsp;Christell van der Vyver,&nbsp;Pedri Claassens,&nbsp;Jens Kossmann,&nbsp;Michaela Fischer-Stettler,&nbsp;Samuel C. Zeeman,&nbsp;James R. Lloyd","doi":"10.1002/biot.70051","DOIUrl":"https://doi.org/10.1002/biot.70051","url":null,"abstract":"<p>This study examines how post-transcriptional gene silencing of <i>STARCH BRANCHING ENZYME 1</i> (<i>SBE1</i>) and <i>GLUCAN WATER DIKINASE 1</i> (<i>GWD1</i>) affects the structure and properties of potato tuber starch. Silencing of either gene individually or simultaneously altered starch chemistry physical properties. Repression of <i>StGWD1</i> reduced phosphate content, while repression of <i>StSBE1</i> increased it. The phosphate content of starch isolated from plants where both genes were repressed was increased compared to <i>St</i><i>GWD1</i> repressed lines, but lower than both the <i>SBE1</i> repressed lines and the untransformed control. Constituent chain lengths of starches from all lines were altered, and amylose content was increased in the <i>gwd1</i> and <i>sbe1/gwd1</i> double repressed lines, which also accumulated small numbers of lobed starch granules. Pasting properties were also affected, with starch from <i>StSBE1</i>-repressed lines demonstrating increased peak and trough viscosities and <i>gwd1</i> lines showing decreased peak and trough viscosities, compared with the control. Peak and trough viscosities were lowest in the <i>sbe1/gwd1</i> repressed lines. We believe that these data demonstrate that alterations in starch phosphate influence the degree of branching within starch and offer a novel in planta strategy for optimizing the industrial properties of potato storage starch.</p>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/biot.70051","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144244232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Tracking Particle-Encapsulated DNA Across the Anion-Exchange Chromatography Fractions of Recombinant Adeno-Associated Virus Using Droplet Digital PCR and High-Throughput Sequencing 利用微滴数字PCR和高通量测序技术在重组腺相关病毒阴离子交换层析部分追踪颗粒封装的DNA
IF 3.2 3区 生物学
Biotechnology Journal Pub Date : 2025-06-09 DOI: 10.1002/biot.70031
Noriko Hashiba, Yuzhe Yuan, Emi Itou-Kudo, Kyoko Masumi-Koizumi, Keisuke Yusa, Kazuhisa Uchida
{"title":"Tracking Particle-Encapsulated DNA Across the Anion-Exchange Chromatography Fractions of Recombinant Adeno-Associated Virus Using Droplet Digital PCR and High-Throughput Sequencing","authors":"Noriko Hashiba,&nbsp;Yuzhe Yuan,&nbsp;Emi Itou-Kudo,&nbsp;Kyoko Masumi-Koizumi,&nbsp;Keisuke Yusa,&nbsp;Kazuhisa Uchida","doi":"10.1002/biot.70031","DOIUrl":"https://doi.org/10.1002/biot.70031","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Introduction</h3>\u0000 \u0000 <p>Safe and effective adeno-associated virus (AAV) vectors are essential for gene therapy. Particle heterogeneity, specifically particle DNA of varying types and sizes, significantly affects recombinant adeno-associated virus (rAAV) performance. Previous studies have identified particle-associated DNAs; however, the specific DNA composition of these mixed populations remains poorly understood. This study aimed to investigate the DNA composition of the isolated subpopulations of rAAV particles obtained through anion exchange (AEX) chromatography.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>RAAV2-ZsGreen1 particles were fractionated on an AEX column, resulting in 12 distinct fractions. We analyzed the DNA composition of these fractions using droplet digital PCR (ddPCR) and MiSeq to identify the incorporated DNA heterogeneity in them.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our findings illustrated a clear trend in which the DNA content increasing in fractions was associated with an increased rAAV genomic DNA ratio of total particle DNA. The particle DNA content increased significantly across fractions from Peak 1 to Peak 2, showing approximately 30,000- and 5000-fold increases for ZsGreen1 (rAAV genome) and <i>amp<sup>R</sup></i> (plasmid impurity), respectively. Notably, in the empty particle subpopulations, the rate of detectable DNA molecules was lower than one DNA fragment per 100 particles, with inverted terminal repeat (ITR) sequences being the most prevalent.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>With the elucidated profile of particle DNAs, this study provides detailed information on particle heterogeneity, shedding light on empty and partial particle formation and impurity DNA incorporation.</p>\u0000 </section>\u0000 </div>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/biot.70031","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144244229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Advancing Protein-Coding RNA Engineering: From Structural Refinement to Biomedical Implementation 推进蛋白质编码RNA工程:从结构改进到生物医学实施
IF 3.2 3区 生物学
Biotechnology Journal Pub Date : 2025-06-09 DOI: 10.1002/biot.70038
Xuan Lu, Shuangpeng Li, Yue Chi, Shuo Lin, Hui Yuan, Zhiyi Lin, Yingying Xiao, Haihua Yin, Xia Zuo, Ruilin Cheng, Jiahui Xi, Min Chen, Qingjian Zou
{"title":"Advancing Protein-Coding RNA Engineering: From Structural Refinement to Biomedical Implementation","authors":"Xuan Lu,&nbsp;Shuangpeng Li,&nbsp;Yue Chi,&nbsp;Shuo Lin,&nbsp;Hui Yuan,&nbsp;Zhiyi Lin,&nbsp;Yingying Xiao,&nbsp;Haihua Yin,&nbsp;Xia Zuo,&nbsp;Ruilin Cheng,&nbsp;Jiahui Xi,&nbsp;Min Chen,&nbsp;Qingjian Zou","doi":"10.1002/biot.70038","DOIUrl":"https://doi.org/10.1002/biot.70038","url":null,"abstract":"<div>\u0000 \u0000 <p>Messenger RNA (mRNA), emerging as a revolutionary therapeutic tool, has shown remarkable potential in diverse fields such as vaccine development, tumor immunotherapy, gene therapy, and protein replacement therapy, attributed to its high programmability and safety. However, traditional engineered mRNA therapeutics encounter obstacles like short half-lives and limited protein expression, which impede their extensive application in the biomedical domain. In recent years, with the progress of RNA modification technologies and the advent of novel RNA techniques, including mRNA, self-amplifying RNA (saRNA), circular RNA (circRNA), and branched RNA (brRNA), researchers have achieved substantial breakthroughs in enhancing RNA stability, prolonging protein expression, and reducing immunogenicity. This article comprehensively reviews the structure, function, optimization strategies, and biomedical applications of these protein-coding RNAs.</p>\u0000 </div>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144244236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Intensification of rAAV Production Based on HEK293 Cell Transient Transfection 瞬时转染HEK293细胞增强rAAV产生的研究
IF 3.2 3区 生物学
Biotechnology Journal Pub Date : 2025-06-09 DOI: 10.1002/biot.70020
Ye Zhang, Emil Sundäng Peters, Olalekan Daramola, Trudy Ann Tucker, Johan Rockberg, Diane Hatton, Véronique Chotteau
{"title":"Intensification of rAAV Production Based on HEK293 Cell Transient Transfection","authors":"Ye Zhang,&nbsp;Emil Sundäng Peters,&nbsp;Olalekan Daramola,&nbsp;Trudy Ann Tucker,&nbsp;Johan Rockberg,&nbsp;Diane Hatton,&nbsp;Véronique Chotteau","doi":"10.1002/biot.70020","DOIUrl":"https://doi.org/10.1002/biot.70020","url":null,"abstract":"<p>Recombinant adeno-associated virus (rAAV) vectors are widely used in gene therapies, but the rapidly increasing global demand has created a significant challenge for rAAV manufacturing, where production capacity remains a critical bottleneck. To address this, strategies to enhance production yields are urgently needed. This study presents an innovative approach to rAAV production using high cell density (HCD) stirred tank perfusion culture. rAAV1 and rAAV9 vectors carrying GFP cargo were used as models, with triple-plasmid transfection performed in suspension HEK293 cells at a high viable cell density of 50 million cells/mL in culture then maintained at ≥ 30 million cells/mL throughout production. Transfection and production parameters were first optimized in a 5 mL pseudo-perfusion spin tube screening system at HCD. A proof-of-concept was then demonstrated by scaling up to a 200 mL stirred tank bioreactor (STR) in perfusion mode. This intensified process achieved rAAV9 production levels per cell comparable to those observed in reference shake flask cultures at 1 million cells/mL. By implementing transfection at very HCD in a perfusion-based STR, this approach has the potential to significantly enhance rAAV volumetric production capacity, providing a promising solution to meet the growing demand for gene therapies.</p>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/biot.70020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144244355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reconstructing an Inducible Homologous Recombination System in Ogataea Polymorpha 多形藤诱导同源重组体系的构建
IF 3.2 3区 生物学
Biotechnology Journal Pub Date : 2025-06-09 DOI: 10.1002/biot.70040
Nan Jia, Xin Ni, Hongying Wang, Yongjin J. Zhou, Jiaoqi Gao
{"title":"Reconstructing an Inducible Homologous Recombination System in Ogataea Polymorpha","authors":"Nan Jia,&nbsp;Xin Ni,&nbsp;Hongying Wang,&nbsp;Yongjin J. Zhou,&nbsp;Jiaoqi Gao","doi":"10.1002/biot.70040","DOIUrl":"https://doi.org/10.1002/biot.70040","url":null,"abstract":"<div>\u0000 \u0000 <p><i>Ogataea polymorpha</i> is a promising host for industrial production due to its broad substrate spectrum, thermotolerance, and high-density fermentation capability. While recombination machinery engineering has improved genome editing via homologous recombination (HR), constitutive expression of HR-related proteins often causes growth defects. In this study, we divided the complex and multistep HR pathway into three stages and systematically evaluated genes under control of a rhamnose-inducible promoter (P<i><sub>LRA3</sub></i>). We reconstructed a dynamically regulated HR repair system through co-expression of genes ScRAD51, ScRAD52, and ScSLX4, achieving HR rates up to 58%—a 2-fold increase over the starting strain. Notably, coordinated expression of these genes enhanced simultaneous deletion of two genes with a positive rate of 29%. Our tools enable precise genome editing while maintaining normal cell growth in <i>O. polymorpha</i>, providing a solid foundation for studying recombination machinery in non-conventional yeasts.</p>\u0000 </div>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144244402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthetic Genetic Circuits Enabled in Komagataella phaffii Through T7 RNAP/CRISPRa System 通过T7 RNAP/CRISPRa系统激活法菲Komagataella的合成遗传电路
IF 3.2 3区 生物学
Biotechnology Journal Pub Date : 2025-06-09 DOI: 10.1002/biot.70036
Shupeng Ruan, Aoxue Wang, Hongyi Zou, Ying Lin, Lei Ye, Shuli Liang
{"title":"Synthetic Genetic Circuits Enabled in Komagataella phaffii Through T7 RNAP/CRISPRa System","authors":"Shupeng Ruan,&nbsp;Aoxue Wang,&nbsp;Hongyi Zou,&nbsp;Ying Lin,&nbsp;Lei Ye,&nbsp;Shuli Liang","doi":"10.1002/biot.70036","DOIUrl":"https://doi.org/10.1002/biot.70036","url":null,"abstract":"<div>\u0000 \u0000 <p>The CRISPR activation (CRISPRa) transcriptional system has become a powerful synthetic biology tool for the regulation of endogenous gene expression, allowing for precise fine-tuning of target genes through the simple modification of sgRNA sequences. In this study, we demonstrate that sgRNAs can be effectively expressed using the T7 transcription system. The insertion of tRNA sequences between PT7 and sgRNAs significantly enhances the efficiency of transcriptional activation. Furthermore, the design of PT7-tRNA-sgRNA arrays facilitates the multiplexed activation of genes. sgRNA expression was regulated by the Tet-on induction system, split-T7 system, and RNA cleavage processing by HH-HDV, resulting in the creation of a Boolean logic gene circuit capable of performing both AND and OR logic operations. Finally, we developed a UPR self-responsive system by utilizing endogenous promoters that are responsive to UPR signals to control the expression of T7 RNAP. This system dynamically regulates the expression of the endogenous HAC1 transcription factor, thus enhancing the secretion of heterologous proteins. The findings from this study highlight the potential of utilizing the T7 transcription system for the construction of genetic circuits, providing a practical toolkit for gene regulation in the industrial <i>Komagataella phaffii</i> strain.</p>\u0000 </div>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144244237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Engineering Saccharomyces Cerevisiae With Novel Functional Xylose Isomerases From Rumen Microbiota for Enhanced Biofuel Production 利用瘤胃微生物群中新型功能木糖异构酶对酿酒酵母进行工程改造,以提高生物燃料产量
IF 3.2 3区 生物学
Biotechnology Journal Pub Date : 2025-06-09 DOI: 10.1002/biot.70050
Beatriz de Oliveira Vargas, Marcelo Falsarella Carazzolle, Juliana Pimentel Galhardo, Juliana José, Brenda Cristina de Souza, Jéssica Batista de Lima Correia, Jade Ribeiro dos Santos, Gonçalo Amarante Guimarães Pereira, Fellipe da Silveira Bezerra de de Mello
{"title":"Engineering Saccharomyces Cerevisiae With Novel Functional Xylose Isomerases From Rumen Microbiota for Enhanced Biofuel Production","authors":"Beatriz de Oliveira Vargas,&nbsp;Marcelo Falsarella Carazzolle,&nbsp;Juliana Pimentel Galhardo,&nbsp;Juliana José,&nbsp;Brenda Cristina de Souza,&nbsp;Jéssica Batista de Lima Correia,&nbsp;Jade Ribeiro dos Santos,&nbsp;Gonçalo Amarante Guimarães Pereira,&nbsp;Fellipe da Silveira Bezerra de de Mello","doi":"10.1002/biot.70050","DOIUrl":"https://doi.org/10.1002/biot.70050","url":null,"abstract":"<p>Xylose metabolism in <i>Saccharomyces cerevisiae</i> remains a significant bottleneck due to the difficulty in identifying functional and efficient xylose isomerases (XI). In the present study, publicly available metagenomic and metatranscriptomic datasets of rumen microbiota from different herbivorous mammals were used to prospect novel XIs sequences. Seven putative XIs from moose, camel, cow, and sheep were cloned into a strain modified for xylose metabolism. Out of those, five XIs demonstrated activity and efficiently converted xylose into xylulose, resulting in ethanol as the final product. A XI from camel rumen microbiota exhibited a K<sub>M</sub> of 16.25 mM, indicating high substrate affinity. The strains expressing enzymes XI11 and XI12, obtained from sheep rumen microbiota, were able to deplete 40 g/L of xylose within 72 and 96 h, achieving theoretical ethanol yields of 90% and 88%, respectively. These results are comparable to those obtained with <i>Orpinomyces sp</i>. ukk1 XI, a benchmark enzyme previously reported as highly efficient in <i>S. cerevisiae</i>. This study also provides the first report on the successful expression of XIs mined from the ruminal microbiotas of sheep and camels in <i>S. cerevisiae</i>, expanding the perspectives for the optimization of fermentation processes and the production of lignocellulosic biofuels from xylose.</p>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/biot.70050","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144244233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Arg128*-Mediated Dual-Substrate Recognition and Dynamic Transport Mechanisms in (R)-ω-Transaminase: Computational Insights and Mutational Profiling Guided Rational Engineering (R) ω-转氨酶中Arg128*介导的双底物识别和动态转运机制:计算见解和突变谱指导的理性工程
IF 3.2 3区 生物学
Biotechnology Journal Pub Date : 2025-05-19 DOI: 10.1002/biot.70032
Jie Chen, Shuai Qiu, Conglin Ju, Dan Wang, Fangfang Fan, Jun Huang
{"title":"Arg128*-Mediated Dual-Substrate Recognition and Dynamic Transport Mechanisms in (R)-ω-Transaminase: Computational Insights and Mutational Profiling Guided Rational Engineering","authors":"Jie Chen,&nbsp;Shuai Qiu,&nbsp;Conglin Ju,&nbsp;Dan Wang,&nbsp;Fangfang Fan,&nbsp;Jun Huang","doi":"10.1002/biot.70032","DOIUrl":"https://doi.org/10.1002/biot.70032","url":null,"abstract":"<div>\u0000 \u0000 <p>ω-Transaminases (ω-TAs) are critical biocatalysts for the asymmetric synthesis of chiral amines, and uniquely accommodate both hydrophobic and hydrophilic substrates through a conserved binding pocket. In this study, we combine computational simulations and site-directed mutagenesis to dissect this dual-function structure of (<i>R</i>)-selective ω-transaminase from <i>Aspergillus terreus</i> (<i>At</i>ATA). Our results reveal that <i>At</i>ATA employs a synergistic mechanism: aromatic residues within the large pocket stabilize hydrophobic substrates via π-driven interactions, while Arg128* dynamically interacts with hydrophilic compounds through hydrogen bonding. Furthermore, the binding pocket of <i>At</i>ATA exhibits remarkable plasticity to accommodate diverse substrates, with the side chain of Arg128* dynamically adjusting its conformation to facilitate the transport of substrates. Mutational profiling, particularly the R128*A mutation, directly validates these mechanistic insights. Our finding reveals the Arg128*-mediated dual-substrate recognition and transport mechanisms, providing a solid theoretical foundation for enhancing the industrial application of transaminases in pharmaceutical synthesis and green chemistry.</p>\u0000 </div>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 5","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144091271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Prediction of pH Gradient Elution of Ion Exchange Chromatography for Antibody Charge Variants Separation Based on Salt Gradient Elution Experiments 基于盐梯度洗脱实验的pH梯度离子交换色谱分离抗体电荷变体的预测
IF 3.2 3区 生物学
Biotechnology Journal Pub Date : 2025-05-16 DOI: 10.1002/biot.70029
Yu-Xin Liao, Ce Shi, Xue-Zhao Zhong, Xu-Jun Chen, Ran Chen, Shan-Jing Yao, Dong-Qiang Lin
{"title":"Prediction of pH Gradient Elution of Ion Exchange Chromatography for Antibody Charge Variants Separation Based on Salt Gradient Elution Experiments","authors":"Yu-Xin Liao,&nbsp;Ce Shi,&nbsp;Xue-Zhao Zhong,&nbsp;Xu-Jun Chen,&nbsp;Ran Chen,&nbsp;Shan-Jing Yao,&nbsp;Dong-Qiang Lin","doi":"10.1002/biot.70029","DOIUrl":"https://doi.org/10.1002/biot.70029","url":null,"abstract":"<div>\u0000 \u0000 <p>Mechanistic modeling of ion exchange chromatography (IEC) is a promising technique to improve process development. However, when considering the pH influence, model prediction becomes challenging due to the multiple pH-dependent parameters and complex interactions. In order to more effectively predict the pH gradient elution behavior, a two-step model calibration strategy was proposed for the pH-dependent steric mass action (SMA) model with the empirical correlations of characteristic charge <i>ν</i> and equilibrium coefficient <i>k</i><sub>eq</sub>. The strategy was verified through a case study of monoclonal antibody charge variants purification with IEC. All nine calibration experiments were conducted using linear salt gradient elution at three fixed pH values. The average root mean square error (RMSE) was 14.28% between the model calculation and experiments. Both <i>ν</i> and ln(<i>k</i><sub>eq</sub>) exhibited good linear correlations with pH (<i>R</i><sup>2</sup> &gt; 0.99). Then, the well-calibrated pH-dependent SMA model showed a satisfactory capability for predicting the pH gradient elution behaviors with an RMSE of 16.18%. Moreover, the model was used for process optimization under different elution modes, including salt gradient, pH gradient, and salt-pH dual gradient, improving the yield from 70.07% to 74.91%. The optimized linear pH gradient elution was verified by experiment (RMSE = 8.30%). Finally, a methodological framework for utilizing the simplified pH-dependent SMA model developed in this work was summarized to explore its practical applications. The two-step calibration strategy proposed significantly alleviates the workload for the pH-dependent IEC modeling. The model-based process optimization effectively enables faster pH-dependent process development with minimal experiments.</p>\u0000 </div>","PeriodicalId":134,"journal":{"name":"Biotechnology Journal","volume":"20 5","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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