IF 4.7

生物设计研究(英文) Pub Date : 2026-02-03 eCollection Date: 2026-03-01 DOI: 10.1016/j.bidere.2026.100072

Xuemei Tan, Xueli Tan, Bowen Wang, Yan Li, Huanan Li, Wanli Cheng, Jiashu Liu, Zhengbing Jiang

{"title":"Efficient synthesis of optically pure D-lactate from mixed sugars by engineered E. coli consortium.","authors":"Xuemei Tan, Xueli Tan, Bowen Wang, Yan Li, Huanan Li, Wanli Cheng, Jiashu Liu, Zhengbing Jiang","doi":"10.1016/j.bidere.2026.100072","DOIUrl":"https://doi.org/10.1016/j.bidere.2026.100072","url":null,"abstract":"In this study, we constructed two engineered E. coli strains that utilized glucose (E. coli GL10) and xylose (E. coli XL12) simultaneously via division of labor. Both two engineered strains blocked the synthetic pathway of several byproducts, including succinate, formate, ethanol, and acetate. XL12 demonstrated the alleviation of carbon catabolite repression effect and the improvement of xylose utilization in mixed sugar. GL10 and XL12 produced D-lactate from glucose and xylose with an optical purity of 100%, respectively. Microbial consortium using GL10 and XL12 with the inoculation ratio of 1:1 achieved complete glucose depletion and 53.21% xylose utilization simultaneously. Notably, when the fermentation was proceeded using mixed sugar for 36 h, the D-lactate titer of the consortium achieved 3.76 g/L, which is 5.96-fold higher than that of the wild-type (WT) fermentation. The effect of shaking speed and inoculum ratio on the fermentation performance were investigated. Specifically, the xylose utilization in the mixed sugars was improved with an increase of shaking speeds from 50 to 250 rpm, while the yield of D-lactate did not further increase at 250 rpm. When the inoculation ratio of GL10 and XL12 was 1:5, the consortium showed better performance in D-lactate production, which was 6.55-fold higher than that of the WT. The consortium was also utilized mixed sugars effectively in corn straw hydrolysate and produced D-lactate of 5.15 g/L, which was 41.87% higher than that of WT. Our study offers a feasible approach via metabolic engineering and artificial consortium construction for bio-based D-lactate production.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"8 1","pages":"100072"},"PeriodicalIF":4.7,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13109302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Heptad insertion extends the E. coli ROP protein by 50. 七tad的插入使大肠杆菌ROP蛋白延长了50%。

IF 4.7

生物设计研究(英文) Pub Date : 2025-12-08 eCollection Date: 2026-03-01 DOI: 10.1016/j.bidere.2025.100061

Ioannis Karageorgos, D Travis Gallagher

{"title":"Heptad insertion extends the E. coli ROP protein by 50.","authors":"Ioannis Karageorgos, D Travis Gallagher","doi":"10.1016/j.bidere.2025.100061","DOIUrl":"https://doi.org/10.1016/j.bidere.2025.100061","url":null,"abstract":"Antibody function involves conformational variability, yet their extreme flexibility complicates measurement of their structure and properties. They also have numerous ligands, suggesting that a rigid bivalent ligand construct of appropriate length could interact with an antibody to reduce its flexibility for imaging, measurement or functional effect. Such a construct would ideally have an inter-ligand spacer that is fairly rigid and with length between 6 and 10 nm. Coiled-coil bundles of alpha helices represent a common motif in protein structure whose relatively simple parallel geometry makes them suitable for rational modification including applications in metrology. In this study, we describe a heptad-insertion heuristic for extending bundles and apply it to the E. coli ROP/ROM protein, which is a 13 kDa, thermostable RNA-binding unit that is naturally a 4-helix dimer and has been engineered to self-associate in various ways to form larger assemblies. We first introduced a tryptophan residue into the core (wild-type lacks tryptophan) to support precise quantitation, and then extended the protein to 150 % of its native length by inserting four helical heptads. We report the engineering process and crystal structures of the tryptophan mutant and the lengthened protein, which also contains a new phenylalanine in the core. Where wild-type has a length of 4.3 nm, the extended variant has length 6.5 nm and may serve as a rigid module for higher order constructs.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"8 1","pages":"100061"},"PeriodicalIF":4.7,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13109292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Establishing Komagataella phaffii as a cell factory for efficient production of chondroitin sulfate. 建立高效生产硫酸软骨素的法菲Komagataella phaffii细胞工厂。

IF 4.7

生物设计研究(英文) Pub Date : 2025-12-02 eCollection Date: 2026-03-01 DOI: 10.1016/j.bidere.2025.100062

Binying Lv, Feng Xiao, Yingjia Pan, Dongfang Li, Jine Li, Chang Dong, Lei Huang, Zhinan Xu, Jiazhang Lian

{"title":"Establishing Komagataella phaffii as a cell factory for efficient production of chondroitin sulfate.","authors":"Binying Lv, Feng Xiao, Yingjia Pan, Dongfang Li, Jine Li, Chang Dong, Lei Huang, Zhinan Xu, Jiazhang Lian","doi":"10.1016/j.bidere.2025.100062","DOIUrl":"https://doi.org/10.1016/j.bidere.2025.100062","url":null,"abstract":"Chondroitin sulfate (CS) is a vital sulfated glycosaminoglycan with essential physiological functions and broad applications in pharmaceuticals and nutraceuticals. Commercial CS production currently relies on extraction from animal tissues, which suffers from raw material scarcity, long production cycles, and safety concerns. Here, an efficient microbial platform for de novo biosynthesis of chondroitin sulfate A (CSA) was established in Komagataella phaffii. The chondroitin biosynthetic pathway was first reconstructed and optimized through rearrangement of three heterologous genes and promoter selection, achieving 927 mg/L unsulfated chondroitin. Functional expression of a chondroitin-4-O-sulfotransferase (CHST11) enabled the biosynthesis of 750.5 mg/L CSA with a sulfation degree of 2.6 %. Replacement of wild-type CHST11 with its engineered mutant (SMp) significantly enhanced sulfation to 12.1 %. Subsequent multi-copy genomic integration of the SMp expression cassette further increased the sulfation degree to 45.0 % while maintaining a high CSA titer of 1.10 g/L in shake flasks. Enhancement of the 3'-phosphoadenosine-5'-phosphosulfate (PAPS) supply, the key cofactor for sulfation, further improved sulfation to 48.0 %. Finally, the optimized strain PM06 achieved a CSA titer of 7.13 g/L with a sulfation degree of 48.4 % in a 5-L fed-batch fermentation, representing the highest microbial CSA production reported to date. This study demonstrates the successful establishment of K. phaffii as a robust cell factory for high-level and high-sulfation production of CSA. The modular engineering strategy described here provides a generalizable framework for balancing multi-enzyme pathways and offers an efficient, non-animal-derived route for the sustainable industrial production of CS.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"8 1","pages":"100062"},"PeriodicalIF":4.7,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13109340/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Advances in luminescence-based tracing technologies: applications and future perspectives. 基于发光的跟踪技术进展：应用和未来展望。

IF 4.7

生物设计研究(英文) Pub Date : 2025-10-31 eCollection Date: 2026-03-01 DOI: 10.1016/j.bidere.2025.100060

Siyuan Sun, Tiange Wang, Yingzi Li, Hao Du

引用次数: 0

Engineering Escherichia coli for the S-selective production of 2-hydroxyisovalerate. 工程大肠杆菌s选择性生产2-羟基异戊酸酯。

IF 4.7

生物设计研究(英文) Pub Date : 2025-10-08 eCollection Date: 2025-12-01 DOI: 10.1016/j.bidere.2025.100059

Peiling Wu, Haofeng Chen, Guojun Yang, Haoyu Qin, Qian Zhang, Yuxin Chen, Dongjiang Lin, Yang Zhang, Shuyong Lin, Shizhen Wang, Jifeng Yuan

{"title":"Engineering Escherichia coli for the S-selective production of 2-hydroxyisovalerate.","authors":"Peiling Wu, Haofeng Chen, Guojun Yang, Haoyu Qin, Qian Zhang, Yuxin Chen, Dongjiang Lin, Yang Zhang, Shuyong Lin, Shizhen Wang, Jifeng Yuan","doi":"10.1016/j.bidere.2025.100059","DOIUrl":"https://doi.org/10.1016/j.bidere.2025.100059","url":null,"abstract":"2-Hydroxyisovalerate (2-HIV) is a value-added chemical that is widely applied in the synthesis of bioactive compounds and polymers. Here, we report an underexplored metabolic route for the de novo production of S-type 2-HIV (S-HIV) in Escherichia coli. In particular, we identified promiscuous activity of 4-hydroxymandelate synthase (HmaS) from Amycolatopsis orientalis towards the conversion of 2-keto-4-methyl-pentanoate (2-KMP, an immediate precursor for L-leucine) to S-HIV. Next, we designed a variant HmaS (S201F) with abolished activity for mandelate and 4-hydroxymandelate synthesis, thereby minimizing byproduct formation. Coupled with systematic optimization of the L-leucine biosynthetic pathway, we achieved de novo production of S-HIV at 8.1 mM (0.95 g/L) in shake flasks and 33.9 mM (4.0 g/L) in 2-L fed-batch fermentation. In summary, this work represents the first time to realize the efficient synthesis of S-configuration 2-HIV in metabolically engineered E. coli.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"7 4","pages":"100059"},"PeriodicalIF":4.7,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13109320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Four enzymes from button bush enable de novo biosynthesis of spirooxindole alkaloids in yeast. 从钮扣灌木中提取的四种酶可以在酵母中重新合成螺菌吲哚生物碱。

IF 4.7

生物设计研究(英文) Pub Date : 2025-09-24 eCollection Date: 2025-12-01 DOI: 10.1016/j.bidere.2025.100049

Alyssa Dawn Seveck, Jacob Owen Perley, Di Gao, Jiazhang Lian, Yang Qu

{"title":"Four enzymes from button bush enable de novo biosynthesis of spirooxindole alkaloids in yeast.","authors":"Alyssa Dawn Seveck, Jacob Owen Perley, Di Gao, Jiazhang Lian, Yang Qu","doi":"10.1016/j.bidere.2025.100049","DOIUrl":"https://doi.org/10.1016/j.bidere.2025.100049","url":null,"abstract":"Oxindoles are a structurally unique subclass of monoterpenoid indole alkaloids (MIAs) with significant medicinal values such as neuroprotective and anticancer properties and are predominantly found in the Rubiaceae plant family. Recent research has only just begun to uncover the biosynthetic pathways of this complex MIA subclass. Here, we report the discovery, characterization, and functional reconstitution of a four-enzyme pathway from Cephalanthus occidentalis (button bush) that enables the complete de novo biosynthesis of heteroyohimbine-type oxindole alkaloids in engineered yeast. Through transcriptomic mining and biochemical validation, we identified and characterized an ajmalicine synthase (CoAJS), a heteroyohimbine/yohimbine/corynanthe C3-oxidase (CoHYC3O), a C3-reductase (CoHYC3R), and an oxindole synthase (CoOIS) capable of converting strictosidine aglycone into 3-epi-ajmalicine and subsequently into the oxindole alkaloids mitraphylline and isomitraphylline. Saturation kinetics of CoOIS revealed comparable catalytic efficiencies for 3-epi-ajmalicine and its C20 epimer akuammigine, indicating substrate tolerance within the heteroyohimbine subclass. Yeast-based reconstruction of the pathway successfully yielded both mitraphylline epimers and the spirooxindole uncarine F. This work elucidates the enzymatic logic behind oxindole formation and expands the toolkit for MIA scaffold diversification and synthetic biology.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"7 4","pages":"100049"},"PeriodicalIF":4.7,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13109334/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

De novo biosynthesis of Astragalus bioactive isoflavonoid calycosin-7-glucoside in yeast. 黄芪生物活性异黄酮毛蕊异黄酮-7-葡萄糖苷在酵母中的新合成。

IF 4.7

生物设计研究(英文) Pub Date : 2025-09-24 eCollection Date: 2025-12-01 DOI: 10.1016/j.bidere.2025.100058

Cong Chen, Tengfei Liu, Ying Huang, Jiazhang Lian

{"title":"De novo biosynthesis of Astragalus bioactive isoflavonoid calycosin-7-glucoside in yeast.","authors":"Cong Chen, Tengfei Liu, Ying Huang, Jiazhang Lian","doi":"10.1016/j.bidere.2025.100058","DOIUrl":"https://doi.org/10.1016/j.bidere.2025.100058","url":null,"abstract":"Isoflavonoids, such as calycosin-7-glucoside, possess significant pharmaceutical value but are typically sourced from plants, where production is limited by slow growth and complex isolation process. Here, we engineered Saccharomyces cerevisiae for heterologous production of calycosin-7-glucoside. First, via the introduction of isoflavone 4'-O-methyltransferase from Pueraria montana var. lobata (PlOMT9), isoflavone-3'-hydroxylase from Astragalus membranaceus (AmI3'H), and calycosin 7'-O-glucosyltransferase from A. membranaceus (AmUCGT) into our previously constructed daidzein-producing strain, we achieved de novo biosynthesis of calycosin-7-glucoside for the first time. Then, we disrupted the endogenous glucoside hydrolase (EXG1 knockout), enhanced UDP-glucose supply (UGP1 overexpression), and screened a glycosyltransferase (AmUGT88E29 from A. membranaceus) with higher catalytic activity to substantially improve the production of our target compound. Using LC-MS-based metabolomics, we analyzed pathway intermediates and metabolic flux distribution, revealing PlOMT9 as the major bottleneck. Subsequent optimization of PlOMT9 gene copy number further enhanced bioproduction of calycosin-7-glucoside, achieving a final titer of 0.22 mg/L. This study establishes a yeast-based platform for high-value isoflavonoid biosynthesis and provides a foundation for future pathway optimization.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"7 4","pages":"100058"},"PeriodicalIF":4.7,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13109333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Protein design drives synthetic biology research of plant natural products. 蛋白质设计推动了植物天然产物的合成生物学研究。

IF 4.7

生物设计研究(英文) Pub Date : 2025-09-18 eCollection Date: 2025-12-01 DOI: 10.1016/j.bidere.2025.100048

Xiaopeng Zhang, Yinying Yao, Ye Wang, Yongshuo Ma, Yi Shang

{"title":"Protein design drives synthetic biology research of plant natural products.","authors":"Xiaopeng Zhang, Yinying Yao, Ye Wang, Yongshuo Ma, Yi Shang","doi":"10.1016/j.bidere.2025.100048","DOIUrl":"https://doi.org/10.1016/j.bidere.2025.100048","url":null,"abstract":"Plant natural products (PNPs) are widely used in pharmaceutical, cosmetic, and food industries. Currently, their commercial supply largely relies on plant extraction, yet, suffers from low yield and limited resources. Synthetic biology provides a promising solution by reconstituting biosynthetic pathways of PNPs in microbial systems. However, unknown enzymatic steps or poor functional performance of plant-derived enzymes often make it particularly challenging for the PNPs production in microorganisms. To address these limitations, much progress has been made in enzyme mining, enzymatic mechanism elucidation, and enzyme optimization by protein design technologies. The deep integration of artificial intelligence and synthetic biology has provided attractive solutions for the sustainable production of PNPs. This review introduces the cutting-edge advances of protein design technologies in PNPs biosynthesis, elaborates on the approaches to resolve the main bottlenecks in PNPs biosynthesis, and discusses the immense application potential driven by the integration of AI and synthetic biology.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"7 4","pages":"100048"},"PeriodicalIF":4.7,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13109297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790300","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification and engineering of a UDP-rhamnosyltransferase from Trillium tschonoskii for heterologous biosynthesis of polyphyllin Ⅱ in yeast. 酵母中异源合成多叶毛素Ⅱ的鼠李糖苷转移酶的鉴定与工程。

IF 4.7

生物设计研究(英文) Pub Date : 2025-09-14 eCollection Date: 2025-12-01 DOI: 10.1016/j.bidere.2025.100047

Yuxin Yang, Haowen Wang, Ziya Wu, Xing Wang, Yuru Tong, Wei Huang, Xuan Liu, Huan Zhao, Juan Guo, Yating Hu, Xianan Zhang

{"title":"Identification and engineering of a UDP-rhamnosyltransferase from Trillium tschonoskii for heterologous biosynthesis of polyphyllin Ⅱ in yeast.","authors":"Yuxin Yang, Haowen Wang, Ziya Wu, Xing Wang, Yuru Tong, Wei Huang, Xuan Liu, Huan Zhao, Juan Guo, Yating Hu, Xianan Zhang","doi":"10.1016/j.bidere.2025.100047","DOIUrl":"https://doi.org/10.1016/j.bidere.2025.100047","url":null,"abstract":"Polyphyllins, a class of isospirostan-type steroidal saponins, exhibit cytotoxicity against a wide range of cancer cells. Despite extensive research, the complete biosynthetic pathway of these compounds remains elusive. To investigate these pathways, various tissues from Trillium tschonoskii were collected for sequencing, yielding 173,382 high-quality unigene sequences, including 353 annotated as glycosyltransferases. Subsequently, a novel rhamnosyltransferase gene, UGT738A3, was characterized, which catalyzes the conversion of triglycoside polyphyllin III and pennogenin 3-O-beta-chacotrioside into tetraglycoside polyphyllin II and polyphyllin VII. The key residues that affect the catalytic activity of UGT738A3 were identified using site-directed mutation. The catalytic activity of the A158T/P101L mutant toward polyphyllin III and pennogenin 3-O-beta-chacotrioside improved by 2.5- and 6.5-fold, respectively. Therefore, we successfully reconstructed the biosynthesis pathway of polyphyllin Ⅱ in yeast by introducing UGT93M3, which catalyzes the formation of polyphyllin III, and UGT738A3A158T/P101L, achieving a yield of 0.13 mg/L. This study not only investigated the pivotal role of UGT738A3 in the catalysis of tetraglycoside formation but also revealed highly efficient enzymatic components essential for the heterologous biosynthesis of polyphyllin saponins.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"7 4","pages":"100047"},"PeriodicalIF":4.7,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13109326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Advances in the microbial biosynthesis of ʟ-tryptophan and its derivatives. -色氨酸及其衍生物的微生物合成研究进展。

IF 4.7

生物设计研究(英文) Pub Date : 2025-09-13 eCollection Date: 2025-12-01 DOI: 10.1016/j.bidere.2025.100046

Honghao Li, Jiaming Zhang, Jiaxin Gao, Yunzi Luo

引用次数: 0

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