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SCRaMbLE drive application of synthetic yeast genome

Jin Jin, Yuan Ma, Duo Liu

《化学科学与工程前沿（英文）》 2018年 第12卷 第4期   页码 832-834 doi: 10.1007/s11705-018-1749-0

摘要：
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Use of dry yeast cells as a cheap nitrogen source for lactic acid production by thermophilic

Kim Yng Ooi, Jin Chuan Wu

《化学科学与工程前沿（英文）》 2015年 第9卷 第3期   页码 381-385 doi: 10.1007/s11705-015-1534-2

摘要： Dry yeast cells (DYC) were used as a cheap nitrogen source to replace expensive yeast extract (YE) for L-lactic acid production by thermophilic . Cassava starch (200 g·L ) was converted to L-lactic acid by simultaneous saccharification and fermentation using WCP10-4 at 50 °C in the presence of 20 g·L of DYC, giving 148.1 g·L of L-lactic acid at 27 h with a productivity of 5.5 g·L ·h and a yield of 92%. In contrast, 154.4 g·L of lactic acid was produced at 24 h with a productivity of 6.4 g·L ·h and a yield of 96% when equal amount of YE was used under the same conditions. Use of pre-autolyzed DYC at 50 °C for overnight slightly improved the lactic acid titer (154.5 g·L ) and productivity (7.7 g·L ·h ) but gave the same yield (96%).

关键词： L-lactic acid     thermophilic strain     Bacillus coagulans     dry yeast cells     autolysis     fermentation    

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following mutagenesis at two sites near the catalytic pocket and the application of peroxidase-coated yeast

Karla Ilić Đurđić, Raluca Ostafe, Olivera Prodanović, Aleksandra Đurđević Đelmaš, Nikolina Popović, Rainer Fischer, Stefan Schillberg, Radivoje Prodanović

《环境科学与工程前沿（英文）》 2021年 第15卷 第2期 doi: 10.1007/s11783-020-1311-4

摘要： Abstract • Mutations in Lignin peroxidase Trp171 environment improved azo dyes degradation. • Expression on yeast cell surface and cell lysis allowed reusability of biocatalyst. • Aga2-LiP chimeric variants were characterized. The enzymatic degradation of azo dyes is a promising alternative to ineffective chemical and physical remediation methods. Lignin peroxidase (LiP) from Phanerochaete chrysosporium is a heme-containing lignin-degrading oxidoreductase that catalyzes the peroxide-dependent oxidation of diverse molecules, including industrial dyes. This enzyme is therefore ideal as a starting point for protein engineering. Accordingly, we subjected two positions (165 and 264) in the environment of the catalytic Trp171 residue to saturation mutagenesis, and the resulting library of 104 independent clones was expressed on the surface of yeast cells. This yeast display library was used for the selection of variants with the ability to break down structurally-distinct azo dyes more efficiently. We identified mutants with up to 10-fold greater affinity than wild-type LiP for three diverse azo dyes (Evans blue, amido black 10B and Guinea green) and up to 13-fold higher catalytic activity. Additionally, cell wall fragments displaying mutant LiP enzymes were prepared by toluene-induced cell lysis, achieving significant increases in both enzyme activity and stability compared to a whole-cell biocatalyst. LiP-coated cell wall fragments retained their initial dye degradation activity after 10 reaction cycles each lasting 8 h. The best-performing mutants removed up to 2.5-fold more of each dye than the wild-type LiP in multiple reaction cycles.

关键词： Bioremediation     Enzyme immobilization     Protein engineering     Yeast surface display.    

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Inter-chromosomal insertions into wild-type chromosomes induced by SCRaMbLE

《化学科学与工程前沿（英文）》 doi: 10.1007/s11705-024-2458-5

摘要： Genomic rearrangements play a crucial role in shaping biological phenotypic diversity and driving species evolution. Synthetic chromosome rearrangement and modification by LoxP-mediated evolution (SCRaMbLE) has been applied to explore large-scale genomic rearrangements, yet it has been observed that these rearrangements occur exclusively in genomic regions containing loxPsym sites. Here, we found that SCRaMbLE of synthetic yeast harboring synthetic chromosome V and X can generate a variety of synthetic segment insertions into wild-type chromosomes, ranging from 1 to 300 kb. Furthermore, it was revealed that the novel insertions impacted the transcriptional level of neighboring regions and affected the production of exemplar pathway of zeaxanthin. Collectively, our results improve the understanding of the ability of SCRaMbLE to generate complex structural variations in nonsynthetic regions and provide a potential model to explore genomic transposable events.

关键词： genomic rearrangements     synthetic yeast genome     SCRaMbLE     inter-chromosomal insertions     synthetic biology    

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A cytoprotective graphene oxide-polyelectrolytes nanoshell for single-cell encapsulation

Luanying He, Yulin Chang, Junhao Zhu, Ying Bi, Wenlin An, Yiyang Dong, Jia-Hui Liu, Shihui Wang

《化学科学与工程前沿（英文）》 2021年 第15卷 第2期   页码 410-420 doi: 10.1007/s11705-020-1950-9

摘要： Graphene oxide (GO) has been increasingly utilized in the fields of food, biomedicine, environment and other fields because of its benign biocompatible. We encapsulated two kinds of GO with different sizes on yeast cells with the assistance of polyelectrolytes poly (styrene sulfonic acid) sodium salt (PSS) and polyglutamic acid (PGA) (termed as Y@GO). The result does not show a significant difference between the properties of the two types of Y@GO (namely Y@GO1 and Y@GO2). The encapsulation layers are optimized as Yeast/PGA/PSS/PGA/GO/PGA/PSS based on the morphology, dispersity, colony-forming unit, and zeta potential. The encapsulation of GO increases the roughness of the yeast. It is proved that the Y@GO increases the survival time and enhance the activity of yeast cells. The GO shell improves the resistance of yeast cells against pH and salt stresses and extends the storage time of yeast cells.

关键词： GO     yeast     polyelectrolyte     cytoprotection     nanomaterials    

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In vitro agonistic and antagonistic endocrine disrupting effects of organic extracts from waste water of different treatment processes

Kaifeng RAO, Na LI, Mei MA, Zijian WANG

《环境科学与工程前沿（英文）》 2014年 第8卷 第1期   页码 69-78 doi: 10.1007/s11783-013-0502-7

摘要： Effluents from wastewater treatment plant (WWTP) have been reported to have a broad spectrum of endocrine disrupting compounds (EDCs). The majority of studies have focused on the occurrence of estrogenic activity, while ignoring nuclear hormone receptors (NRs) pathways. In the present study, a battery of in vitro yeast bioassays and a cell bioassay, including antagonistic and agonistic effects on estrogen receptor (ER), androgen receptor (AR), progesterone receptor (PR), estrogen-related receptor (ERR) and aryl hydrocarbon receptor (AHR), were conducted to evaluate the removal efficiencies of EDCs by different treatment processes of a WWTP located in Beijing. Estrogenic, anti-estrogenic, anti- androgenic, anti-progesteronic, anti-ERR and the activation of AHR activities were detected in samples from all treatment processes and the receiving water. The concentration of estrogenic contaminants with estradiol (E ) equivalent concentrations ranged from 0.82 × 10 to 3.54 × 10 g E -EQ·L . The concentration of anti-estrogenic contaminants with 4-hydroxytamoxifen (4-OHT) equivalent concentrations ranged from 1.24 × 10 to 2.36 × 10 g 4-OHT-EQ·L . The concentration of anti-androgenic contaminants ranged from 2.21 × 10 to 3.52 × 10 g flutamide-EQ·L . The concentration of anti-progesteronic contaminants ranged from 3.15 × 10 to 2.71 × 10 g RU486-EQ·L . The concentration of anti-ERR contaminants ranged from 7.09 × 10 to 6.50 × 10 g 4-OHT-EQ·L . The concentration of AHR activators ranged from 1.7 × 10 to 3.4 × 10 g TCDD-EQ·L . These processes including secondary clarifier, coagulation, as well as coal and sand filtration could eliminated 67.2% of estrogenic contaminants, 47.0% of anti-estrogenic contaminants, 98.3% of anti-androgenic contaminants, 88.4% of anti-progesteronic contaminants, 65.4% of anti-ERR contaminants and 46.9% of AHR activators. WWTP effluents contain multiple receptor disruptors may have very complex adverse effects on exposed organisms.

关键词： waste water     in vitro     recombinant yeast assay     ethoxyresorufin-O-deethylase (EROD)     receptor     endocrine    

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PtHAK5, a candidate for mediating high-affinity K

Haili YANG, Weidan ZHANG, Weiwei CHAI, Wenying WANG, Li GAO, Jing ZHANG, Yongping WANG, Suo-Min WANG

《农业科学与工程前沿（英文）》 2018年 第5卷 第1期   页码 108-117 doi: 10.15302/J-FASE-2018200

摘要： is a typical salt-exclu-ding halophytic grass with strong salt-tolerance, which enhances tolerance by restricting Na influx as well as having a strong selectivity for K over Na . The HAK5 K transporters generally modulate effective K acquisition in plants, especially under low K condition. In this study, from was isolated by RT-PCR and characterized using yeast complementation. The results showed PtHAK5 consisted of 784 amino acids and shared over 80% homology with the identified high-affinity K transporter HAK5 from other higher plants. The expression of rescued the K -uptake-defective phenotype of yeast strain CY162. In conclusion, PtHAK5 is a candidate for mediating high-affinity K uptake under low K conditions.

关键词： K+ uptake     PtHAK5     Puccinellia tenuiflora     yeast complementation    

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Construction, characterization and application of a genome-wide promoter library in

Ting Yuan,Yakun Guo,Junkai Dong,Tianyi Li,Tong Zhou,Kaiwen Sun,Mei Zhang,Qingyu Wu,Zhen Xie,Yizhi Cai,Limin Cao,Junbiao Dai

《化学科学与工程前沿（英文）》 2017年 第11卷 第1期   页码 107-116 doi: 10.1007/s11705-017-1621-7

摘要： Promoters are critical elements to control gene expression but could behave differently under various growth conditions. Here we report the construction of a genome-wide promoter library, in which each native promoter in was cloned upstream of a yellow fluorescent protein (YFP) reporter gene. Nine libraries were arbitrarily defined and assembled in bacteria. The resulting pools of promoters could be prepared and transformed into a yeast strain either as centromeric plasmids or integrated into a genomic locus upon enzymatic treatment. Using fluorescence activated cell sorting, we classified the yeast strains based on YFP fluorescence intensity and arbitrarily divided the entire library into 12 bins, representing weak to strong promoters. Several strong promoters were identified from the most active bins and their activities were assayed under different growth conditions. Finally, these promoters were applied to drive the expression of genes in xylose utilization to improve fermentation efficiency. Together, this library could provide a quick solution to identify and utilize desired promoters under user-defined growth conditions.

关键词： synthetic biology     yeast     promoter activity     metabolic engineering     xylose utilization    

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糖基工程毕赤酵母制备的SARS-CoV-2 S蛋白RBD受体结合区亚单位疫苗可激发中和抗体反应 Article

刘波, 殷瑛, 刘雨潇, 王甜甜, 孙鹏, 欧阳秦, 巩新, 侯旭宸, 张军, 任洪广, ​​​​​​​罗士强, 柯倩, 姚咏明, 徐俊杰, 吴军

《工程（英文）》 2022年 第13卷 第6期   页码 107-115 doi: 10.1016/j.eng.2021.06.012

摘要：

2020年至今，新型冠状病毒SARS-CoV-2已经在全球大流行。新冠疫苗被寄于厚望用以减轻防控压力，成为解决疫情危机的有效手段之一。SARS-CoV-2通过S蛋白受体结合区RBD与宿主细胞ACE2受体结合侵染机体。本文提供了一种利用新型糖基工程毕赤酵母表达系统，制备基于S蛋白RBD重组亚单位候选疫苗的方法。该糖基工程酵母的糖基化修饰途径经过人源化改造后，具有类似于哺乳动物细胞糖基化修饰特点。研究发现，RBD候选疫苗可以有效地诱导小鼠产生高滴度的抗RBD特异性抗体，含Al(OH)3和CpG双佐剂的RBD免疫组小鼠产生的特异性抗体滴度和病毒中和抗体滴度显著地高于Al(OH)3单佐剂组，且中和抗体可以在小鼠体内持续6个月以上。综上所述，本文利用糖基工程酵母制备了SARS-CoV-2 S蛋白RBD糖蛋白疫苗，该疫苗能够诱导小鼠产生高滴度中和抗体，同时提供了一种可制备具有无岩藻糖的复杂型N-糖基化修饰重组蛋白的方法。

关键词： 冠状病毒     SARS-CoV-2     疫苗     酵母     受体结合区（RBD）    

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标题 作者 时间 类型 操作

SCRaMbLE drive application of synthetic yeast genome

Jin Jin, Yuan Ma, Duo Liu

期刊论文

Use of dry yeast cells as a cheap nitrogen source for lactic acid production by thermophilic

Kim Yng Ooi, Jin Chuan Wu

期刊论文

following mutagenesis at two sites near the catalytic pocket and the application of peroxidase-coated yeast

Karla Ilić Đurđić, Raluca Ostafe, Olivera Prodanović, Aleksandra Đurđević Đelmaš, Nikolina Popović, Rainer Fischer, Stefan Schillberg, Radivoje Prodanović

期刊论文

Inter-chromosomal insertions into wild-type chromosomes induced by SCRaMbLE

期刊论文

A cytoprotective graphene oxide-polyelectrolytes nanoshell for single-cell encapsulation

Luanying He, Yulin Chang, Junhao Zhu, Ying Bi, Wenlin An, Yiyang Dong, Jia-Hui Liu, Shihui Wang

期刊论文

In vitro agonistic and antagonistic endocrine disrupting effects of organic extracts from waste water of different treatment processes

Kaifeng RAO, Na LI, Mei MA, Zijian WANG

期刊论文

PtHAK5, a candidate for mediating high-affinity K

Haili YANG, Weidan ZHANG, Weiwei CHAI, Wenying WANG, Li GAO, Jing ZHANG, Yongping WANG, Suo-Min WANG

期刊论文

Construction, characterization and application of a genome-wide promoter library in

Ting Yuan,Yakun Guo,Junkai Dong,Tianyi Li,Tong Zhou,Kaiwen Sun,Mei Zhang,Qingyu Wu,Zhen Xie,Yizhi Cai,Limin Cao,Junbiao Dai

期刊论文

糖基工程毕赤酵母制备的SARS-CoV-2 S蛋白RBD受体结合区亚单位疫苗可激发中和抗体反应

刘波, 殷瑛, 刘雨潇, 王甜甜, 孙鹏, 欧阳秦, 巩新, 侯旭宸, 张军, 任洪广, ​​​​​​​罗士强, 柯倩, 姚咏明, 徐俊杰, 吴军

期刊论文