Pub Date : 2024-11-22DOI: 10.1016/j.synbio.2024.11.005
Yue Wu , Guang-Qing Du , Dong-Han Ma , Jin-Long Li , Huan Fang , Hui-Na Dong , Zhao-Xia Jin , Da-Wei Zhang
Biotin (vitamin B7) is a crucial cofactor for various metabolic processes and has significant applications in pharmaceuticals, cosmetics, and animal feed. Bacillus subtilis, a well-studied Gram-positive bacterium, presents a promising host for biotin production due to its Generally Recognized as Safe (GRAS) status, robust genetic tractability, and capacity for metabolite secretion. This study focuses on the metabolic engineering of B. subtilis to enhance biotin biosynthesis. Initially, the desthiobiotin (DTB) and biotin synthesis ability of different B. subtilis strains were evaluated to screen for suitable chassis cells. Subsequently, the titers of DTB and biotin were increased to 21.6 mg/L and 2.7 mg/L, respectively, by relieving the feedback repression of biotin synthesis and deleting the biotin uptake protein YhfU. Finally, through engineering the access tunnel to the active site of biotin synthase (BioB) for reactants and modulating its expression, the biotin titer was increased to 11.2 mg/L, marking an 1130-fold improvement compared to the wild-type strain. These findings provide novel strategies for enhancing the production of DTB and improving the conversion efficiency of DTB to biotin.
{"title":"Pathway and protein channel engineering of Bacillus subtilis for improved production of desthiobiotin and biotin","authors":"Yue Wu , Guang-Qing Du , Dong-Han Ma , Jin-Long Li , Huan Fang , Hui-Na Dong , Zhao-Xia Jin , Da-Wei Zhang","doi":"10.1016/j.synbio.2024.11.005","DOIUrl":"10.1016/j.synbio.2024.11.005","url":null,"abstract":"<div><div>Biotin (vitamin B<sub>7</sub>) is a crucial cofactor for various metabolic processes and has significant applications in pharmaceuticals, cosmetics, and animal feed. <em>Bacillus subtilis</em>, a well-studied Gram-positive bacterium, presents a promising host for biotin production due to its Generally Recognized as Safe (GRAS) status, robust genetic tractability, and capacity for metabolite secretion. This study focuses on the metabolic engineering of <em>B</em>. <em>subtilis</em> to enhance biotin biosynthesis. Initially, the desthiobiotin (DTB) and biotin synthesis ability of different <em>B</em>. <em>subtilis</em> strains were evaluated to screen for suitable chassis cells. Subsequently, the titers of DTB and biotin were increased to 21.6 mg/L and 2.7 mg/L, respectively, by relieving the feedback repression of biotin synthesis and deleting the biotin uptake protein YhfU. Finally, through engineering the access tunnel to the active site of biotin synthase (BioB) for reactants and modulating its expression, the biotin titer was increased to 11.2 mg/L, marking an 1130-fold improvement compared to the wild-type strain. These findings provide novel strategies for enhancing the production of DTB and improving the conversion efficiency of DTB to biotin.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 307-313"},"PeriodicalIF":4.4,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142745797","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}
Pub Date : 2024-11-19DOI: 10.1016/j.synbio.2024.11.004
Yanting Cao , Jianghua Li , Long Liu , Guocheng Du , Yanfeng Liu
Metabolic engineering-driven microbial cell factories have made great progress in the efficient bioproduction of biochemical and recombinant proteins. However, the low efficiency and robustness of microbial cell factories limit their industrial applications. Harnessing microbial heterogeneity contributes to solving this. In this review, the origins of microbial heterogeneity and its effects on biosynthesis are first summarized. Synthetic biology-driven tools and strategies that can be used to improve biosynthesis by increasing and reducing microbial heterogeneity are then systematically summarized. Next, novel single-cell technologies available for unraveling microbial heterogeneity and facilitating heterogeneity regulation are discussed. Furthermore, a combined workflow of increasing genetic heterogeneity in the strain-building step to help in screening highly productive strains - reducing heterogeneity in the production process to obtain highly robust strains (IHP-RHR) facilitated by single-cell technologies was proposed to obtain highly productive and robust strains by harnessing microbial heterogeneity. Finally, the prospects and future challenges are discussed.
{"title":"Harnessing microbial heterogeneity for improved biosynthesis fueled by synthetic biology","authors":"Yanting Cao , Jianghua Li , Long Liu , Guocheng Du , Yanfeng Liu","doi":"10.1016/j.synbio.2024.11.004","DOIUrl":"10.1016/j.synbio.2024.11.004","url":null,"abstract":"<div><div>Metabolic engineering-driven microbial cell factories have made great progress in the efficient bioproduction of biochemical and recombinant proteins. However, the low efficiency and robustness of microbial cell factories limit their industrial applications. Harnessing microbial heterogeneity contributes to solving this. In this review, the origins of microbial heterogeneity and its effects on biosynthesis are first summarized. Synthetic biology-driven tools and strategies that can be used to improve biosynthesis by increasing and reducing microbial heterogeneity are then systematically summarized. Next, novel single-cell technologies available for unraveling microbial heterogeneity and facilitating heterogeneity regulation are discussed. Furthermore, a combined workflow of increasing genetic heterogeneity in the strain-building step to help in screening highly productive strains - reducing heterogeneity in the production process to obtain highly robust strains (IHP-RHR) facilitated by single-cell technologies was proposed to obtain highly productive and robust strains by harnessing microbial heterogeneity. Finally, the prospects and future challenges are discussed.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 281-293"},"PeriodicalIF":4.4,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142745795","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}
Pub Date : 2024-11-14DOI: 10.1016/j.synbio.2024.11.003
Feng Xu, Kaihao Hu, Ali Mohsin, Jie Wu, Lihuan Su, Yuan Wang, Rong Ben, Hao Gao, Xiwei Tian, Ju Chu
Gentamicin, an aminoglycoside antibiotic, is generated by a few species within the genus Micromonospora and has garnered significant attention due to its broad-spectrum efficacy in combating numerous infectious diseases. Comprising a complex array of closely related aminoglycoside compounds, the gentamicin B and C complexes emerge as particularly pertinent in clinical contexts. This review outlines the latest advancements in the biosynthesis and production of gentamicin, commencing with a comprehensive overview of its biosynthetic pathway. Subsequently, the article encapsulates a spectrum of strategies currently deployed to augment gentamicin yields. These strategies include mutation screening, molecular biological techniques, and optimization of the fermentation process. Moreover, numerous methods have been documented for detecting gentamicin across a range of matrices, underscoring the significance of precise quantitative analysis. Finally, the review furnishes an exhaustive market analysis and future outlook, elucidating prevailing trends and challenges within the gentamicin industry. Overall, this article serves as a pivotal resource for researchers and professionals engaged in gentamicin research, furnishing a meticulous introduction to efficient synthesis technologies and diverse applications, alongside presenting innovative concepts and methodologies aimed at increasing gentamicin production.
庆大霉素是一种氨基糖苷类抗生素，由小单胞菌属中的少数几个物种产生，因其在抗击多种传染病方面的广谱疗效而备受关注。庆大霉素 B 和 C 复合物由一系列密切相关的氨基糖苷化合物组成，在临床上尤为重要。本综述概述了庆大霉素生物合成和生产方面的最新进展，首先对其生物合成途径进行了全面概述。随后，文章概述了目前为提高庆大霉素产量而采取的一系列策略。这些策略包括突变筛选、分子生物学技术和发酵过程优化。此外，文章还介绍了在各种基质中检测庆大霉素的多种方法，强调了精确定量分析的重要性。最后，综述提供了详尽的市场分析和未来展望，阐明了庆大霉素行业的当前趋势和挑战。总之，这篇文章为从事庆大霉素研究的研究人员和专业人士提供了重要的资源，细致地介绍了高效合成技术和各种应用，同时提出了旨在提高庆大霉素产量的创新概念和方法。
{"title":"Recent advances in the biosynthesis and production optimization of gentamicin: A critical review","authors":"Feng Xu, Kaihao Hu, Ali Mohsin, Jie Wu, Lihuan Su, Yuan Wang, Rong Ben, Hao Gao, Xiwei Tian, Ju Chu","doi":"10.1016/j.synbio.2024.11.003","DOIUrl":"10.1016/j.synbio.2024.11.003","url":null,"abstract":"<div><div>Gentamicin, an aminoglycoside antibiotic, is generated by a few species within the genus <em>Micromonospora</em> and has garnered significant attention due to its broad-spectrum efficacy in combating numerous infectious diseases. Comprising a complex array of closely related aminoglycoside compounds, the gentamicin B and C complexes emerge as particularly pertinent in clinical contexts. This review outlines the latest advancements in the biosynthesis and production of gentamicin, commencing with a comprehensive overview of its biosynthetic pathway. Subsequently, the article encapsulates a spectrum of strategies currently deployed to augment gentamicin yields. These strategies include mutation screening, molecular biological techniques, and optimization of the fermentation process. Moreover, numerous methods have been documented for detecting gentamicin across a range of matrices, underscoring the significance of precise quantitative analysis. Finally, the review furnishes an exhaustive market analysis and future outlook, elucidating prevailing trends and challenges within the gentamicin industry. Overall, this article serves as a pivotal resource for researchers and professionals engaged in gentamicin research, furnishing a meticulous introduction to efficient synthesis technologies and diverse applications, alongside presenting innovative concepts and methodologies aimed at increasing gentamicin production.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 247-261"},"PeriodicalIF":4.4,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142699561","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}
Pub Date : 2024-11-09DOI: 10.1016/j.synbio.2024.11.001
Haoran Shi , Jiabin Wang , Shanshan Li , Chongxi Liu , Lei Li , Zhuoxu Dong , Lan Ye , Xiangjing Wang , Yanyan Zhang , Wensheng Xiang
Guvermectin, a purine nucleoside natural product produced by the genus Streptomyces, has recently been registered as a new biopesticide to boost rice yield. Despite its economic and agricultural significance, the regulatory mechanisms of guvermectin biosynthesis remain essentially unknown, hindering industrial production and widespread agricultural application. Here, we examined the roles of two LacI family regulators, gvmR and gvmR2, located within and adjacent to the guvermectin biosynthesis cluster, respectively, in guvermectin production in Streptomyces caniferus NEAU6. GvmR activated the expression of the guvermectin cluster by binding to the promoters of gvmR, gvmA, and O1, while GvmR2 repressed the guvermectin cluster via competitive binding to promoters containing GvmR-binding sites, specifically, a 14-bp palindromic sequences: 5′-RTCATWCGYATGAY-3′ (R = G/A, W = A/T, Y = T/C). Moreover, GvmR indirectly activates the expression of gvmR2 while GvmR2 feedback inhibits gvmR transcription, suggesting a functional interaction between the two regulators for coordinating guvermectin production. Overexpression of gvmR via the T7 RNA polymerase-T7 promoter system in the gvmR2 mutant significantly elevated guvermectin production by 125 % (from 631 mg L−1 to 1422 mg L−1), compared to the parental strain NEAU6. This suggested that combinatorial manipulation of gvmR and gvmR2 is useful for improving guvermectin production. These findings enrich our knowledge of the regulatory network for guvermectin biosynthesis, and offer key targets and effective strategies for high-titer guvermectin production.
{"title":"Coordinated regulation of two LacI family regulators, GvmR and GvmR2, on guvermectin production in Streptomyces caniferus","authors":"Haoran Shi , Jiabin Wang , Shanshan Li , Chongxi Liu , Lei Li , Zhuoxu Dong , Lan Ye , Xiangjing Wang , Yanyan Zhang , Wensheng Xiang","doi":"10.1016/j.synbio.2024.11.001","DOIUrl":"10.1016/j.synbio.2024.11.001","url":null,"abstract":"<div><div>Guvermectin, a purine nucleoside natural product produced by the genus S<em>treptomyces</em>, has recently been registered as a new biopesticide to boost rice yield. Despite its economic and agricultural significance, the regulatory mechanisms of guvermectin biosynthesis remain essentially unknown, hindering industrial production and widespread agricultural application. Here, we examined the roles of two LacI family regulators, <em>gvmR</em> and <em>gvmR2</em>, located within and adjacent to the guvermectin biosynthesis cluster, respectively, in guvermectin production in <em>Streptomyces caniferus</em> NEAU6. GvmR activated the expression of the guvermectin cluster by binding to the promoters of <em>gvmR</em>, <em>gvmA</em>, and <em>O1</em>, while GvmR2 repressed the guvermectin cluster via competitive binding to promoters containing GvmR-binding sites, specifically, a 14-bp palindromic sequences: 5′-RTCATWCGYATGAY-3′ (R = G/A, W = A/T, Y = T/C). Moreover, GvmR indirectly activates the expression of <em>gvmR2</em> while GvmR2 feedback inhibits <em>gvmR</em> transcription, suggesting a functional interaction between the two regulators for coordinating guvermectin production. Overexpression of <em>gvmR</em> via the T7 RNA polymerase-T7 promoter system in the <em>gvmR2</em> mutant significantly elevated guvermectin production by 125 % (from 631 mg L<sup>−1</sup> to 1422 mg L<sup>−1</sup>), compared to the parental strain NEAU6. This suggested that combinatorial manipulation of <em>gvmR</em> and <em>gvmR2</em> is useful for improving guvermectin production. These findings enrich our knowledge of the regulatory network for guvermectin biosynthesis, and offer key targets and effective strategies for high-titer guvermectin production.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 237-246"},"PeriodicalIF":4.4,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142699560","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}
Pub Date : 2024-11-09DOI: 10.1016/j.synbio.2024.10.007
Yaping Mao , Jiangming Zhu , Qian Zhang , Guangyi Wang , Hongkai Fan , Xiaowei Zhang , Yuwei Sun , Yong Wang
Phenylethylisoquinoline alkaloids (PIAs) are medicinally important natural products derived from the 1-phenylethylisoquinoline precursor. Heterologous production of the PIAs remains challenging due to the incomplete elucidation of biosynthetic pathway and the lack of proper microbial cell factory designed for precursor enhancement. In this work, an artificial pathway composed of eight enzymes from different species was established for de novo 1-phenylethylisoquinoline biosynthesis in engineered Escherichia coli. The yield of the intermediate 4-hydroxydihydrocinnamaldehyde was optimized through screening various NADP+-dependent 2-alkenal reductases, cofactor regeneration and the site-directed mutagenesis of key residues in ChAER1. Subsequently, incorporation of the modified dopamine pathway into an endogenous reductase-deficient E. coli with high tyrosine yield boosted the production of 1-phenylethylisoquinoline, reaching 402.58 mg/L in a 5L fermenter. Our work lays a foundation for the future large-scale production of high value-added 1-phenylethylisoquinoline-related alkaloids.
{"title":"De novo synthesis of 1-phenethylisoquinoline in engineered Escherichia coli","authors":"Yaping Mao , Jiangming Zhu , Qian Zhang , Guangyi Wang , Hongkai Fan , Xiaowei Zhang , Yuwei Sun , Yong Wang","doi":"10.1016/j.synbio.2024.10.007","DOIUrl":"10.1016/j.synbio.2024.10.007","url":null,"abstract":"<div><div>Phenylethylisoquinoline alkaloids (PIAs) are medicinally important natural products derived from the 1-phenylethylisoquinoline precursor. Heterologous production of the PIAs remains challenging due to the incomplete elucidation of biosynthetic pathway and the lack of proper microbial cell factory designed for precursor enhancement. In this work, an artificial pathway composed of eight enzymes from different species was established for de novo 1-phenylethylisoquinoline biosynthesis in engineered <em>Escherichia coli</em>. The yield of the intermediate 4-hydroxydihydrocinnamaldehyde was optimized through screening various NADP<sup>+</sup>-dependent 2-alkenal reductases, cofactor regeneration and the site-directed mutagenesis of key residues in ChAER1. Subsequently, incorporation of the modified dopamine pathway into an endogenous reductase-deficient <em>E. coli</em> with high tyrosine yield boosted the production of 1-phenylethylisoquinoline, reaching 402.58 mg/L in a 5L fermenter. Our work lays a foundation for the future large-scale production of high value-added 1-phenylethylisoquinoline-related alkaloids.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 271-280"},"PeriodicalIF":4.4,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142699564","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}
Pub Date : 2024-11-08DOI: 10.1016/j.synbio.2024.11.002
Wei Huang , Xingzhi Jiao , Lingqi Hua , Qianjin Kang , Lili Zhang , Xiaoxia Luo , Linquan Bai
Natural products (NPs) afforded by living-beings, especially by microscopic species, represent invaluable and indispensable reservoirs for drug leads in clinical practice. With the rapid advancement in sequencing technology and bioinformatics, the ever-increasing number of microbial biosynthetic gene clusters (BGCs) were decrypted, while a great deal of BGCs remain cryptic or inactive under standard laboratory culture conditions. Addressing this dilemma requires innovative tactics to awaken quiescence of BGCs by releasing the potential of microbial secondary metabolism for mining novel NPs. In this study, a universal strategy was proposed to induce the expression of silent BGCs by leveraging the dynamic interactions among coexisting microbial neighbors within a microbiota. This approach involves the deconstruction/reconstruction of binary interactions among the coexisting neighbors to create a pipeline for BGCs arousing. Coupled with the acquisition of 2760 microbial individuals from the Apocynum venetum (Luobuma, LBM) phyllosphere in a successive dilution procedure, 44 culturable isolates were screened using binary interaction, in which 12.6 % pairs demonstrated potent mutual interacting effects. Furthermore, after selecting the four most promising isolates, a full-scale metabolic inspection was conducted, in which 25.3 % of the interacting pairs showcased significant metabolomic variations with de-cryptic activities. Notably, with the aid of visualization of IMS technology, one of the physiologically functional entities, the bactericidal agent resistomycin, was elucidated from the core interacting pair between the co-culture of the Streptomyces sp. LBM_605 and the Rhodococcus sp. LBM_791. This study highlights the intrinsic interactions among coexisting microorganisms within a phyllosphere microbiota as novel avenues for exploring and harnessing NPs.
{"title":"Harnessing the microbial interactions from Apocynum venetum phyllosphere for natural product discovery","authors":"Wei Huang , Xingzhi Jiao , Lingqi Hua , Qianjin Kang , Lili Zhang , Xiaoxia Luo , Linquan Bai","doi":"10.1016/j.synbio.2024.11.002","DOIUrl":"10.1016/j.synbio.2024.11.002","url":null,"abstract":"<div><div>Natural products (NPs) afforded by living-beings, especially by microscopic species, represent invaluable and indispensable reservoirs for drug leads in clinical practice. With the rapid advancement in sequencing technology and bioinformatics, the ever-increasing number of microbial biosynthetic gene clusters (BGCs) were decrypted, while a great deal of BGCs remain cryptic or inactive under standard laboratory culture conditions. Addressing this dilemma requires innovative tactics to awaken quiescence of BGCs by releasing the potential of microbial secondary metabolism for mining novel NPs. In this study, a universal strategy was proposed to induce the expression of silent BGCs by leveraging the dynamic interactions among coexisting microbial neighbors within a microbiota. This approach involves the deconstruction/reconstruction of binary interactions among the coexisting neighbors to create a pipeline for BGCs arousing. Coupled with the acquisition of 2760 microbial individuals from the <em>Apocynum venetum</em> (Luobuma, LBM) phyllosphere in a successive dilution procedure, 44 culturable isolates were screened using binary interaction, in which 12.6 % pairs demonstrated potent mutual interacting effects. Furthermore, after selecting the four most promising isolates, a full-scale metabolic inspection was conducted, in which 25.3 % of the interacting pairs showcased significant metabolomic variations with de-cryptic activities. Notably, with the aid of visualization of IMS technology, one of the physiologically functional entities, the bactericidal agent resistomycin, was elucidated from the core interacting pair between the co-culture of the <em>Streptomyces</em> sp. LBM_605 and the <em>Rhodococcus</em> sp. LBM_791. This study highlights the intrinsic interactions among coexisting microorganisms within a phyllosphere microbiota as novel avenues for exploring and harnessing NPs.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 262-270"},"PeriodicalIF":4.4,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142699563","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}
Pub Date : 2024-10-28DOI: 10.1016/j.synbio.2024.10.006
Dongming Sun , Longhao Wu , Xiaocong Lu , Chenhao Li , Lili Xu , Hongxing Li , Deyun He , Aiqun Yu , Tao Yu , Jianzhi Zhao , Hongting Tang , Xiaoming Bao
Presently, Saccharomyces cerevisiae demonstrates proficient co-fermentation of glucose and xylose, marking a significant advancement in second-generation fuel ethanol production. However, the presence of high concentrations of inhibitors in industrial lignocellulose hydrolysates and post-glucose effect caused by glucose consumption hinders severely impedes yeast robustness and xylose utilization for ethanol fermentation. Even worse, the antagonism between xylose utilization ability and strain robustness was observed, which proposes a difficult challenge in the production of second-generation fuel ethanol by S. cerevisiae. This review introduces the effect of engineering transcriptional regulatory networks on enhancing xylose utilization, improving strain robustness, alleviating antagonism between xylose utilization and strain robustness, and reducing post-glucose effect. Additionally, we provide an outlook on the developmental trends in this field, offering insights into future directions for increasing the production of second-generation fuel ethanol in S. cerevisiae.
目前，酿酒酵母能熟练地同时发酵葡萄糖和木糖，这标志着第二代燃料乙醇生产取得了重大进展。然而，工业木质纤维素水解物中存在的高浓度抑制剂以及葡萄糖消耗引起的后葡萄糖效应严重阻碍了酵母的生长和利用木糖发酵乙醇。更为严重的是，木糖利用能力与菌株的稳健性之间存在拮抗作用，这为利用酿酒酵母生产第二代燃料乙醇提出了艰巨的挑战。本综述介绍了转录调控网络工程对提高木糖利用率、改善菌株稳健性、缓解木糖利用率与菌株稳健性之间的拮抗作用以及降低葡萄糖后效应的影响。此外，我们还对这一领域的发展趋势进行了展望，为提高 S. cerevisiae 第二代燃料乙醇产量的未来方向提供了见解。
{"title":"Engineering transcriptional regulatory networks for improving second-generation fuel ethanol production in Saccharomyces cerevisiae","authors":"Dongming Sun , Longhao Wu , Xiaocong Lu , Chenhao Li , Lili Xu , Hongxing Li , Deyun He , Aiqun Yu , Tao Yu , Jianzhi Zhao , Hongting Tang , Xiaoming Bao","doi":"10.1016/j.synbio.2024.10.006","DOIUrl":"10.1016/j.synbio.2024.10.006","url":null,"abstract":"<div><div>Presently, <em>Saccharomyces cerevisiae</em> demonstrates proficient co-fermentation of glucose and xylose, marking a significant advancement in second-generation fuel ethanol production. However, the presence of high concentrations of inhibitors in industrial lignocellulose hydrolysates and post-glucose effect caused by glucose consumption hinders severely impedes yeast robustness and xylose utilization for ethanol fermentation. Even worse, the antagonism between xylose utilization ability and strain robustness was observed, which proposes a difficult challenge in the production of second-generation fuel ethanol by <em>S. cerevisiae</em>. This review introduces the effect of engineering transcriptional regulatory networks on enhancing xylose utilization, improving strain robustness, alleviating antagonism between xylose utilization and strain robustness, and reducing post-glucose effect. Additionally, we provide an outlook on the developmental trends in this field, offering insights into future directions for increasing the production of second-generation fuel ethanol in <em>S. cerevisiae</em>.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 207-217"},"PeriodicalIF":4.4,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142586524","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}
Pub Date : 2024-10-26DOI: 10.1016/j.synbio.2024.10.005
Ana-Belén Blázquez, Nereida Jiménez de Oya
Flaviviruses affect the lives of millions of people in endemic regions and also have the potential to impact non-endemic areas. Factors such as climate change, global warming, deforestation, and increased travel and trade are linked to the spread of flaviviruses into new habitats and host species. Given the absence of specific treatments and the limited availability of vaccines, it is imperative to understand the biology of flaviviruses and develop rapid and sensitive diagnostic tests. These measures are essential for preventing the transmission of these potentially life-threatening pathogens. Flavivirus infections are mainly diagnosed using conventional methods. However, these techniques present several drawbacks, including high expenses, time-consuming procedures, and the need for skilled professionals. The search for fast, easy-to-use, and affordable alternative techniques as a feasible solution for developing countries is leading to the search for new methods in the diagnosis of flaviviruses, such as biosensors.
This review provides a comprehensive overview of different biosensor detection strategies for flaviviruses and describes recent advances in diagnostic technologies. Finally, we explore their future prospects and potential applications in pathogen detection. This review serves as a valuable resource to understand advances in ongoing research into new biosensor-based diagnostic methods for flaviviruses.
{"title":"Biosensors for the detection of flaviviruses: A review","authors":"Ana-Belén Blázquez, Nereida Jiménez de Oya","doi":"10.1016/j.synbio.2024.10.005","DOIUrl":"10.1016/j.synbio.2024.10.005","url":null,"abstract":"<div><div>Flaviviruses affect the lives of millions of people in endemic regions and also have the potential to impact non-endemic areas. Factors such as climate change, global warming, deforestation, and increased travel and trade are linked to the spread of flaviviruses into new habitats and host species. Given the absence of specific treatments and the limited availability of vaccines, it is imperative to understand the biology of flaviviruses and develop rapid and sensitive diagnostic tests. These measures are essential for preventing the transmission of these potentially life-threatening pathogens. Flavivirus infections are mainly diagnosed using conventional methods. However, these techniques present several drawbacks, including high expenses, time-consuming procedures, and the need for skilled professionals. The search for fast, easy-to-use, and affordable alternative techniques as a feasible solution for developing countries is leading to the search for new methods in the diagnosis of flaviviruses, such as biosensors.</div><div>This review provides a comprehensive overview of different biosensor detection strategies for flaviviruses and describes recent advances in diagnostic technologies. Finally, we explore their future prospects and potential applications in pathogen detection. This review serves as a valuable resource to understand advances in ongoing research into new biosensor-based diagnostic methods for flaviviruses.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 194-206"},"PeriodicalIF":4.4,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142561287","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}
Pub Date : 2024-10-18DOI: 10.1016/j.synbio.2024.10.004
Mei-Li Sun , Ziyun Zou , Lu Lin , Rodrigo Ledesma-Amaro , Kaifeng Wang , Xiao-Jun Ji
Abscisic acid (ABA) is an important phytohormone with diverse applications. It currently relies on the fermentation of Botrytis cinerea, which suffers from limited availability of genetic engineering tools. Here, Yarrowia lipolytica was engineered to enable de novo biosynthesis of ABA. To overcome the rate-limiting P450 enzymes, systematic engineering strategies were implemented. Firstly, the dissolved oxygen was increased to boost the activity of P450 enzymes. Secondly, the expansion of endoplasmic reticulum was implemented to improve the functional expression of P450 enzymes. Lastly, rate-limiting enzymes were assembled to facilitate substrate trafficking. Moreover, ABA production was further improved by strengthening the mevalonate pathway. Finally, the engineered strain produced 1221.45 mg/L of ABA in a 5-L bioreactor. The study provides effective approaches for alleviating rate-limiting P450 enzymes to enhance ABA production and achieve competitive industrial-level ABA production in Y. lipolytica.
脱落酸（ABA）是一种重要的植物激素，具有多种用途。目前，它依赖于西尼瑞氏菌的发酵，而西尼瑞氏菌的发酵受制于有限的基因工程工具。在这里，我们改造了脂肪分解蓍草菌（Yarrowia lipolytica），使其能够从头开始生物合成 ABA。为了克服 P450 酶的速率限制，我们实施了系统工程策略。首先，增加溶解氧以提高 P450 酶的活性。其次，扩大内质网以提高 P450 酶的功能表达。最后，组装限速酶以促进底物的运输。此外，还通过加强甲羟戊酸途径进一步提高了 ABA 的产量。最后，工程菌株在 5 升生物反应器中产生了 1221.45 毫克/升的 ABA。这项研究提供了有效的方法来减轻限速 P450 酶的作用，从而提高脂溶性酵母菌的 ABA 产量，并实现具有竞争力的工业级 ABA 生产。
{"title":"Systematic metabolic engineering of Yarrowia lipolytica for efficient production of phytohormone abscisic acid","authors":"Mei-Li Sun , Ziyun Zou , Lu Lin , Rodrigo Ledesma-Amaro , Kaifeng Wang , Xiao-Jun Ji","doi":"10.1016/j.synbio.2024.10.004","DOIUrl":"10.1016/j.synbio.2024.10.004","url":null,"abstract":"<div><div>Abscisic acid (ABA) is an important phytohormone with diverse applications. It currently relies on the fermentation of <em>Botrytis cinerea</em>, which suffers from limited availability of genetic engineering tools. Here, <em>Yarrowia lipolytica</em> was engineered to enable <em>de novo</em> biosynthesis of ABA. To overcome the rate-limiting P450 enzymes, systematic engineering strategies were implemented. Firstly, the dissolved oxygen was increased to boost the activity of P450 enzymes. Secondly, the expansion of endoplasmic reticulum was implemented to improve the functional expression of P450 enzymes. Lastly, rate-limiting enzymes were assembled to facilitate substrate trafficking. Moreover, ABA production was further improved by strengthening the mevalonate pathway. Finally, the engineered strain produced 1221.45 mg/L of ABA in a 5-L bioreactor. The study provides effective approaches for alleviating rate-limiting P450 enzymes to enhance ABA production and achieve competitive industrial-level ABA production in <em>Y. lipolytica</em>.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 165-173"},"PeriodicalIF":4.4,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142553132","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}
Pub Date : 2024-10-16DOI: 10.1016/j.synbio.2024.10.003
Xinglong Wang , Kangjie Xu , Haoran Fu , Qiming Chen , Beichen Zhao , Xinyi Zhao , Jingwen Zhou
Streptomyces mobaraenesis transglutaminase (smTG) can be used for site-specific labeling of proteins with chemical groups. Here, we explored the use of modified smTG for the biosynthesis of nanobody-fluorophore conjugates (NFC). smTG catalyzes the conjugation of acyl donors containing glutamine with lysine-containing acceptors, which can lead to non-specific cross-linking. To achieve precise site-specific labeling, we employed molecular docking and virtual mutagenesis to redesign the enzyme's substrate specificity towards the peptide GGGGQR, a non-preferred acyl donor for smTG. Starting with a thermostable and highly active smTG variant (TGm2), we identified that single mutations G250H and Y278E significantly enhanced activity against GGGGQR, increasing it by 41 % and 1.13-fold, respectively. Notably, the Y278E mutation dramatically shifted the enzyme's substrate preference, with the activity ratio against GGGGQR versus the standard substrate CBZ-Gln-Gly rising from 0.05 to 0.93. In case studies, we used nanobodies 1C12 and 7D12 as labeling targets, catalyzing their conjugation with a synthetic fluorophore via smTG variants. Nanobodies fused with GGGGQR were successfully site-specifically labeled by TGm2-Y278E, in contrast to non-specific labeling observed with other variants. These results suggest that engineering smTG for site-specific labeling is a promising approach for the biosynthesis of antibody-drug conjugates.
{"title":"Enhancing substrate specificity of microbial transglutaminase for precise nanobody labeling","authors":"Xinglong Wang , Kangjie Xu , Haoran Fu , Qiming Chen , Beichen Zhao , Xinyi Zhao , Jingwen Zhou","doi":"10.1016/j.synbio.2024.10.003","DOIUrl":"10.1016/j.synbio.2024.10.003","url":null,"abstract":"<div><div><em>Streptomyces mobaraenesis</em> transglutaminase (smTG) can be used for site-specific labeling of proteins with chemical groups. Here, we explored the use of modified smTG for the biosynthesis of nanobody-fluorophore conjugates (NFC). smTG catalyzes the conjugation of acyl donors containing glutamine with lysine-containing acceptors, which can lead to non-specific cross-linking. To achieve precise site-specific labeling, we employed molecular docking and virtual mutagenesis to redesign the enzyme's substrate specificity towards the peptide GGGGQR, a non-preferred acyl donor for smTG. Starting with a thermostable and highly active smTG variant (TGm2), we identified that single mutations G250H and Y278E significantly enhanced activity against GGGGQR, increasing it by 41 % and 1.13-fold, respectively. Notably, the Y278E mutation dramatically shifted the enzyme's substrate preference, with the activity ratio against GGGGQR versus the standard substrate CBZ-Gln-Gly rising from 0.05 to 0.93. In case studies, we used nanobodies 1C12 and 7D12 as labeling targets, catalyzing their conjugation with a synthetic fluorophore via smTG variants. Nanobodies fused with GGGGQR were successfully site-specifically labeled by TGm2-Y278E, in contrast to non-specific labeling observed with other variants. These results suggest that engineering smTG for site-specific labeling is a promising approach for the biosynthesis of antibody-drug conjugates.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 185-193"},"PeriodicalIF":4.4,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142553134","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}
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