Engineering Microbiology最新文献_第8页

CRISPRi screen highlights chromatin regulation to be involved in formic acid tolerance in Saccharomyces cerevisiae CRISPRi筛选突出了酿酒酵母中涉及甲酸耐受性的染色质调节

Engineering Microbiology Pub Date : 2023-06-01 DOI: 10.1016/j.engmic.2023.100076

Vaskar Mukherjee , Ibai Lenitz , Ulrika Lind , Anders Blomberg , Yvonne Nygård

{"title":"CRISPRi screen highlights chromatin regulation to be involved in formic acid tolerance in Saccharomyces cerevisiae","authors":"Vaskar Mukherjee , Ibai Lenitz , Ulrika Lind , Anders Blomberg , Yvonne Nygård","doi":"10.1016/j.engmic.2023.100076","DOIUrl":"https://doi.org/10.1016/j.engmic.2023.100076","url":null,"abstract":"<div>Formic acid is one of the main weak acids in lignocellulosic hydrolysates that is known to be inhibitory to yeast growth even at low concentrations. In this study, we employed a CRISPR interference (CRISPRi) strain library comprising >9000 strains encompassing >98% of all essential and respiratory growth-essential genes, to study formic acid tolerance in Saccharomyces cerevisiae. To provide quantitative growth estimates on formic acid tolerance, the strains were screened individually on solid medium supplemented with 140 mM formic acid using the Scan-o-Matic platform. Selected resistant and sensitive strains were characterized in liquid medium supplemented with formic acid and in synthetic hydrolysate medium containing a combination of inhibitors. Strains with gRNAs targeting genes associated with chromatin remodeling were significantly enriched for strains showing formic acid tolerance. In line with earlier findings on acetic acid tolerance, we found genes encoding proteins involved in intracellular vesicle transport enriched among formic acid sensitive strains. The growth of the strains in synthetic hydrolysate medium followed the same trend as when screened in medium supplemented with formic acid. Strains sensitive to formic acid had decreased growth in the synthetic hydrolysate and all strains that had improved growth in the presence of formic acid also grew better in the hydrolysate medium. Systematic analysis of CRISPRi strains allowed identification of genes involved in tolerance mechanisms and provided novel engineering targets for bioengineering strains with increased resistance to inhibitors in lignocellulosic hydrolysates.</div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"3 2","pages":"Article 100076"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49890674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Applications of toxin-antitoxin systems in synthetic biology 毒素-抗毒素系统在合成生物学中的应用

Engineering Microbiology Pub Date : 2023-06-01 DOI: 10.1016/j.engmic.2023.100069

Jianzhong Lin , Yunxue Guo , Jianyun Yao , Kaihao Tang , Xiaoxue Wang

{"title":"Applications of toxin-antitoxin systems in synthetic biology","authors":"Jianzhong Lin , Yunxue Guo , Jianyun Yao , Kaihao Tang , Xiaoxue Wang","doi":"10.1016/j.engmic.2023.100069","DOIUrl":"https://doi.org/10.1016/j.engmic.2023.100069","url":null,"abstract":"<div>Toxin-antitoxin (TA) systems are ubiquitous in bacteria and archaea. Most are composed of two neighboring genetic elements, a stable toxin capable of inhibiting crucial cellular processes, including replication, transcription, translation, cell division and membrane integrity, and an unstable antitoxin to counteract the toxicity of the toxin. Many new discoveries regarding the biochemical properties of the toxin and antitoxin components have been made since the first TA system was reported nearly four decades ago. The physiological functions of TA systems have been hotly debated in recent decades, and it is now increasingly clear that TA systems are important immune systems in prokaryotes. In addition to being involved in biofilm formation and persister cell formation, these modules are antiphage defense systems and provide host defenses against various phage infections via abortive infection. In this review, we explore the potential applications of TA systems based on the recent progress made in elucidating TA functions. We first describe the most recent classification of TA systems and then introduce the biochemical functions of toxins and antitoxins, respectively. Finally, we primarily focus on and devote considerable space to the application of TA complexes in synthetic biology.</div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"3 2","pages":"Article 100069"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49890677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Microbial Technology for Biosustainability 生物可持续性的微生物技术

Engineering Microbiology Pub Date : 2023-06-01 DOI: 10.1016/j.engmic.2023.100088

Wensheng Qin , Guodong Liu

引用次数: 0

Genetic manipulation and tools in myxobacteria for the exploitation of secondary metabolism 利用黏菌进行二次代谢的遗传操作和工具

Engineering Microbiology Pub Date : 2023-06-01 DOI: 10.1016/j.engmic.2023.100075

Xinjing Yue, Duohong Sheng, Li Zhuo, Yue-Zhong Li

引用次数: 2

Prospects for engineering Ralstonia eutropha and Zymomonas mobilis for the autotrophic production of 2,3-butanediol from CO2 and H2 从CO2和H2自养生产2,3-丁二醇的工程研究进展

Engineering Microbiology Pub Date : 2023-06-01 DOI: 10.1016/j.engmic.2023.100074

Hui Wei , Wei Wang , Yat-Chen Chou , Michael E. Himmel , Xiaowen Chen , Yannick J. Bomble , Min Zhang

{"title":"Prospects for engineering Ralstonia eutropha and Zymomonas mobilis for the autotrophic production of 2,3-butanediol from CO2 and H2","authors":"Hui Wei , Wei Wang , Yat-Chen Chou , Michael E. Himmel , Xiaowen Chen , Yannick J. Bomble , Min Zhang","doi":"10.1016/j.engmic.2023.100074","DOIUrl":"https://doi.org/10.1016/j.engmic.2023.100074","url":null,"abstract":"<div>The decarbonization of the chemical industry and a shift toward circular economies because of high global CO2 emissions make CO2 an attractive feedstock for manufacturing chemicals. Moreover, H2 is a low-cost and carbon-free reductant because technologies such as solar-driven electrolysis and supercritical water (scH2O) gasification enable sustainable production of molecular hydrogen (H2). We review the recent advances in engineering Ralstonia eutropha, the representative species of “Knallgas” bacteria, for utilizing CO2 and H2 to autotrophically produce 2,3-butanediol (2,3-BDO). This assessment is focused on state-of-the-art approaches for splitting H2 to supply energy in the form of ATP and NADH to power cellular reactions and employing the Calvin-Benson-Bassham cycle for CO2 fixation. Major challenges and opportunities for application and future perspectives are discussed in the context of developing other promising CO2 and H2-utilizing microorganisms, exemplified by Zymomonas mobilis.</div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"3 2","pages":"Article 100074"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49890678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Global regulation of fungal secondary metabolism in Trichoderma reesei by the transcription factor Ypr1, as revealed by transcriptome analysis 转录组分析揭示了转录因子Ypr1对里氏木霉真菌次生代谢的全局调控

Engineering Microbiology Pub Date : 2023-06-01 DOI: 10.1016/j.engmic.2022.100065

Jie Yang, Jia-Xiang Li, Fei Zhang, Xin-Qing Zhao

{"title":"Global regulation of fungal secondary metabolism in Trichoderma reesei by the transcription factor Ypr1, as revealed by transcriptome analysis","authors":"Jie Yang, Jia-Xiang Li, Fei Zhang, Xin-Qing Zhao","doi":"10.1016/j.engmic.2022.100065","DOIUrl":"https://doi.org/10.1016/j.engmic.2022.100065","url":null,"abstract":"<div>Trichoderma reesei Rut-C-30 is a well-known robust producer of cellulolytic enzymes, which are used to degrade lignocellulosic biomass for the sustainable production of biofuels and biochemicals. However, studies of its secondary metabolism and regulation remain scarce. Ypr1 was previously described as a regulator of the biosynthesis of the yellow pigment sorbicillin (a bioactive agent with great pharmaceutical interest) in T. reesei and several other fungi. However, the manner in which this regulator affects global gene transcription has not been explored. In this study, we report the effect of Ypr1 on the regulation of both the secondary and primary metabolism of T. reesei Rut-C30. A global gene transcription profile was obtained using a comparative transcriptomic analysis of the wild-type strain T. reesei Rut-C-30 and its ypr1 deletion mutant. The results of this analysis suggest that, in addition to its role in regulating sorbicillin and the major extracellular (hemi)cellulases, Ypr1 also affects the transcription of genes encoding several other secondary metabolites. Although the primary metabolism of T. reesei ∆ypr1 became less active compared with that of T. reesei Rut-C-30, several gene clusters involved in its secondary metabolism were activated, such as the gene clusters for the biosynthesis of specific polyketides and non-ribosomal peptides, together with the “sorbicillinoid–cellulase” super cluster, indicating that specific secondary metabolites and cellulases may be co-regulated in T. reesei Rut-C-30. The results presented in this study may benefit the development of genetic engineering strategies for the production of sorbicillin by T. reesei Rut-C-30, and provide insights for enhancing sorbicillin production in other filamentous fungal producers.</div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"3 2","pages":"Article 100065"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49890673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Advances on the biosynthesis of pyridine rings 吡啶环生物合成研究进展

Engineering Microbiology Pub Date : 2023-06-01 DOI: 10.1016/j.engmic.2022.100064

Carolina E. Portero , Yong Han , M. Raquel Marchán-Rivadeneira

引用次数: 0

A highly selective cell-based fluorescent biosensor for genistein detection 染料木黄酮检测的高选择性细胞荧光生物传感器

Engineering Microbiology Pub Date : 2023-06-01 DOI: 10.1016/j.engmic.2023.100078

Lucy Fang-I Chao , Dany Liu , Verena Siewers

{"title":"A highly selective cell-based fluorescent biosensor for genistein detection","authors":"Lucy Fang-I Chao , Dany Liu , Verena Siewers","doi":"10.1016/j.engmic.2023.100078","DOIUrl":"https://doi.org/10.1016/j.engmic.2023.100078","url":null,"abstract":"<div>Genistein, an isoflavone found mainly in legumes, has been shown to have numerous health benefits for humans. Therefore, there is substantial interest in producing it using microbial cell factories. To aid in screening for high genistein producing microbial strains, a cell-based biosensor for genistein was developed by repurposing the Gal4DBD-ERα-VP16 (GEV) transcriptional activator in Saccharomyces cerevisiae. In the presence of genistein, the GEV sensor protein binds to the GAL1 promoter and activates transcription of a downstream GFP reporter. The performance of the biosensor, as measured by fold difference in GFP signal intensity after external genistein induction, was improved by engineering the sensor protein, its promoter and the reporter promoter. Biosensor performance increased when the weak promoter REV1p was used to drive GEV sensor gene expression and the VP16 transactivating domain on GEV was replaced with the tripartite VPR transactivator that had its NLS removed. The biosensor performance further improved when the binding sites for the inhibitor Mig1 were removed from and two additional Gal4p binding sites were added to the reporter promoter. After genistein induction, our improved biosensor output a GFP signal that was 20 times higher compared to the uninduced state. Out of the 8 flavonoids tested, the improved biosensor responded only to genistein and in a somewhat linear manner. The improved biosensor also responded to genistein produced in vivo, with the GFP reporter intensity directly proportional to intracellular genistein concentration. When combined with fluorescence-based cell sorting technology, this biosensor could facilitate high-throughput screening of a genistein-producing yeast cell factory.</div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"3 2","pages":"Article 100078"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49890676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Fungal arginine-containing cyclodipeptide synthases are finally revealed 真菌含精氨酸环二肽合成酶的最终揭示

Engineering Microbiology Pub Date : 2023-06-01 DOI: 10.1016/j.engmic.2023.100080

Hang Li

引用次数: 0

Yeast surface display of leech hyaluronidase for the industrial production of hyaluronic acid oligosaccharides 水蛭透明质酸酶的酵母表面展示用于透明质酸低聚糖的工业化生产

Engineering Microbiology Pub Date : 2023-04-05 DOI: 10.1016/j.engmic.2023.100086

Lizhi Liao , Hao Huang , Yang Wang , Guocheng Du , Zhen Kang

{"title":"Yeast surface display of leech hyaluronidase for the industrial production of hyaluronic acid oligosaccharides","authors":"Lizhi Liao , Hao Huang , Yang Wang , Guocheng Du , Zhen Kang","doi":"10.1016/j.engmic.2023.100086","DOIUrl":"https://doi.org/10.1016/j.engmic.2023.100086","url":null,"abstract":"<div>Leech hyaluronidase (LHyal) is a hyperactive hyaluronic acid (HA) hydrolase that belongs to the hyaluronoglucuronidase family. Traditionally, LHyal is extracted from the heads of leeches, but the recent development of the Pichia pastoris recombinant LHyal expression method permitted the industrial production of size-specific HA oligosaccharides. However, at present LHyal expressed by recombinant yeast strains requires laborious protein purification steps. Moreover, the enzyme is deactivated and removed after single use. To solve this problem, we developed a recyclable LHyal biocatalyst using a yeast surface display (YSD) system. After screening and characterization, we found that the cell wall protein Sed1p displayed stronger anchoring to the P. pastoris cell wall than other cell wall proteins. By optimizing the type and length of the linkers between LHyal and Sed1p, we increased the activity of enzymes displayed on the P. pastoris cell wall by 50.34% in flask cultures. LHyal-(GGGS)6-Sed1p activity further increased to 3.58 × 105 U mL−1 in fed-batch cultivation in a 5 L bioreactor. Enzymatic property analysis results revealed that the displayed LHyal-(GGGS)6-Sed1p generated the same oligosaccharides but exhibited higher thermal stability than free LHyal enzyme. Moreover, displayed LHyal-(GGGS)6-Sed1p could be recovered easily from HA hydrolysis solutions via low-speed centrifugation and could be reused at least 5 times. YSD of LHyal not only increased the utilization efficiency of the enzyme but also simplified the purification process for HA oligosaccharides. Thus, this study provides an alternative approach for the industrial preparation of LHyal and HA oligosaccharides.</div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"3 4","pages":"Article 100086"},"PeriodicalIF":0.0,"publicationDate":"2023-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50203817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3