Bioengineered bugs最新文献_第3页

Fast track assembly of multigene constructs using Golden Gate cloning and the MoClo system. 利用金门克隆和MoClo系统快速组装多基因构建体。

Bioengineered bugs Pub Date : 2012-01-01 DOI: 10.4161/bbug.3.1.18223

Stefan Werner, Carola Engler, Ernst Weber, Ramona Gruetzner, Sylvestre Marillonnet

{"title":"Fast track assembly of multigene constructs using Golden Gate cloning and the MoClo system.","authors":"Stefan Werner, Carola Engler, Ernst Weber, Ramona Gruetzner, Sylvestre Marillonnet","doi":"10.4161/bbug.3.1.18223","DOIUrl":"https://doi.org/10.4161/bbug.3.1.18223","url":null,"abstract":"Recent progress in the field of synthetic biology has led to the creation of cells containing synthetic genomes. Although these first synthetic organisms contained copies of natural genomes, future work will be directed toward engineering of organisms with modified genomes and novel phenotypes. Much work, however, remains to be done to be able to routinely engineer novel biological functions. As a tool that will be useful for such purpose, we have recently developed a modular cloning system (MoClo) that allows high throughput assembly of multiple genetic elements. We present here new features of this cloning system that allow to increase the speed of assembly of multigene constructs. As an example, 68 DNA fragments encoding basic genetic elements were assembled using three one-pot cloning steps, resulting in a 50 kb construct containing 17 eukaryotic transcription units. This cloning system should be useful for generating the multiple construct variants that will be required for developing gene networks encoding novel functions, and fine-tuning the expression levels of the various genes involved.","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"3 1","pages":"38-43"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.3.1.18223","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30290855","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: 114

Recombinant D. radiodurans cells for bioremediation of heavy metals from acidic/neutral aqueous wastes. 重组耐辐射球菌细胞对酸性/中性水废中重金属的生物修复。

Bioengineered bugs Pub Date : 2012-01-01 DOI: 10.4161/bbug.3.1.18878

Chitra Seetharam Misra, Deepti Appukuttan, Venkata Siva Satyanarayana Kantamreddi, Amara S Rao, Shree Kumar Apte

引用次数: 35

Computational studies on a new cationic peroxidase isoenzyme from artichoke leaves. 洋蓟叶阳离子过氧化物酶同工酶的计算研究。

Bioengineered bugs Pub Date : 2012-01-01 DOI: 10.4161/bbug.3.1.17937

Angela Cardinali, Isabella D'Antuono, Benny Danilo Belviso, Rocco Caliandro

引用次数: 0

Biomedicals from a soil bug: expanding scFv production host range. 来自土壤细菌的生物医学:扩大scFv生产宿主范围。

Bioengineered bugs Pub Date : 2012-01-01 DOI: 10.4161/bbug.3.1.17739

Thorben Dammeyer

引用次数: 0

Bench-top fermentative production of plant benzylisoquinoline alkaloids using a bacterial platform. 利用细菌平台台式发酵生产植物苯基异喹啉生物碱。

Bioengineered bugs Pub Date : 2012-01-01 DOI: 10.4161/bbug.3.1.18446

Akira Nakagawa, Hiromichi Minami, Ju-Sung Kim, Takashi Koyanagi, Takane Katayama, Fumihiko Sato, Hidehiko Kumagai

{"title":"Bench-top fermentative production of plant benzylisoquinoline alkaloids using a bacterial platform.","authors":"Akira Nakagawa, Hiromichi Minami, Ju-Sung Kim, Takashi Koyanagi, Takane Katayama, Fumihiko Sato, Hidehiko Kumagai","doi":"10.4161/bbug.3.1.18446","DOIUrl":"https://doi.org/10.4161/bbug.3.1.18446","url":null,"abstract":"The plant secondary metabolites benzylisoquinoline alkaloids (BIAs) have diverse pharmaceutical activities, and some are used medicinally (e.g., morphine, codeine, berberine). Recently, we constructed a platform to produce BIAs using bioengineered Escherichia coli, which could be useful for bulk production. The E. coli strain used in this system produces the important intermediate (S)-reticuline from glucose or glycerol. Although the amount produced (40 mg/L) exceeded the amount that can be purified from plants, the conversion efficiency from glycerol was only 0.15%; thus, there was much room for improvement. Our production system was developed in a jar fermenter but it is difficult to work with multiple samples using this system. In contrast, many samples can be cultured in parallel using shake flask cultures, allowing optimization of production conditions. Here, we describe bench-top production of (S)-reticuline and optimization of culture conditions using shake flask cultures. The production of (S)-reticuline reached 33.9 mg/L.","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"3 1","pages":"49-53"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.3.1.18446","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30333392","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: 21

Molecular diagnostics: the changing culture of medical microbiology. 分子诊断学:医学微生物培养的变化。

Bioengineered bugs Pub Date : 2012-01-01 DOI: 10.4161/bbug.3.1.19011

Susan Bullman, Brigid Lucey, Roy D Sleator

引用次数: 29

A color-based stable multi-copy integrant selection system for Pichia pastoris using the attenuated ADE1 and ADE2 genes as auxotrophic markers. 以ADE1和ADE2减毒基因为营养不良标记的毕赤酵母彩色稳定多拷贝整合选择系统

Bioengineered bugs Pub Date : 2012-01-01 DOI: 10.4161/bbug.3.1.17936

Min Du, Michael B Battles, Juergen H Nett

{"title":"A color-based stable multi-copy integrant selection system for Pichia pastoris using the attenuated ADE1 and ADE2 genes as auxotrophic markers.","authors":"Min Du, Michael B Battles, Juergen H Nett","doi":"10.4161/bbug.3.1.17936","DOIUrl":"https://doi.org/10.4161/bbug.3.1.17936","url":null,"abstract":"The methylotropic yeast Pichia pastoris has been used for more than two decades to successfully produce a large number of recombinant proteins. Currently, a wide variety of auxotrophic and drug based selection markers are employed to screen for clones expressing the protein of interest. For most proteins an increased copy number of the integrated plasmid results in higher levels of expression, but these multi-copy integrants can be unstable due to the propensity of P. pastoris for homologous recombination. Here we describe a multi-copy selection system based on ade1 and ade2 auxotrophic parent strains and the respective attenuated markers with truncated promoter regions. We show that for all four proteins we tested, the use of the attenuated markers leads to increased protein expression when compared with selection based on the full strength markers. The fact that the adenine auxotrophic strains grow more slowly than the complemented counterparts essentially ensures the stability of multi-copy integration. At the same time, the accumulation of a red dye in the auxotrophic strains also provides an easy, color-based selection for transformants with multiple copies.","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"3 1","pages":"32-7"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.3.1.17936","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30290854","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: 29

Differentiation of programmed Arabidopsis cells. 程序化拟南芥细胞的分化。

Bioengineered bugs Pub Date : 2012-01-01 DOI: 10.4161/bbug.3.1.17786

De-Yu Xie, Ming-Zhu Shi

{"title":"Differentiation of programmed Arabidopsis cells.","authors":"De-Yu Xie, Ming-Zhu Shi","doi":"10.4161/bbug.3.1.17786","DOIUrl":"https://doi.org/10.4161/bbug.3.1.17786","url":null,"abstract":"Plants express genes that encode enzymes that catalyse reactions to form plant secondary metabolites in specific cell types. However, the mechanisms of how plants decide their cellular metabolic fate and how cells diversify and specialise their specific secondary metabolites remains largely unknown. Additionally, whether and how an established metabolic program impacts genome-wide reprogramming of plant gene expression is unclear. We recently isolated PAP1-programmed anthocyanin-producing (red) and -free (white) cells from Arabidopsis thaliana; our previous studies have indicated that the PAP1 expression level is similar between these two different cell types. Transcriptional analysis showed that the red cells contain the TTG1-GL3/TT8-PAP1 regulatory complex, which controls anthocyanin biosynthesis; in contrast, the white cells and the wild-type cells lack this entire complex. These data indicate that different regulatory programming underlies the different metabolic states of these cells. In addition, our previous transcriptomic comparison indicated that there is a clear difference in the gene expression profiles of the red and wild-type cells, which is probably a consequence of cell-specific reprogramming. Based on these observations, in this report we discuss the potential mechanisms that underlie the programming and reprogramming of gene expression involved in anthocyanin biosynthesis.","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"3 1","pages":"54-9"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bbug.3.1.17786","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30290848","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: 13

Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome. 人类肠道移动宏基因组中质粒的进化、生态和生物技术观点。

Bioengineered bugs Pub Date : 2012-01-01 DOI: 10.4161/bbug.3.1.17883

Lesley A Ogilvie, Sepinoud Firouzmand, Brian V Jones

{"title":"Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome.","authors":"Lesley A Ogilvie, Sepinoud Firouzmand, Brian V Jones","doi":"10.4161/bbug.3.1.17883","DOIUrl":"10.4161/bbug.3.1.17883","url":null,"abstract":"Numerous mobile genetic elements (MGE) are associated with the human gut microbiota and collectively referred to as the gut mobile metagenome. The role of this flexible gene pool in development and functioning of the gut microbial community remains largely unexplored, yet recent evidence suggests that at least some MGE comprising this fraction of the gut microbiome reflect the co-evolution of host and microbe in the gastro-intestinal tract. In conjunction, the high level of novel gene content typical of MGE coupled with their predicted high diversity, suggests that the mobile metagenome constitutes an immense and largely unexplored gene-space likely to encode many novel activities with potential biotechnological or pharmaceutical value, as well as being important to the development and functioning of the gut microbiota. Of the various types of MGE that comprise the gut mobile metagenome, plasmids are of particular importance since these elements are often capable of autonomous transfer between disparate bacterial species, and are known to encode accessory functions that increase bacterial fitness in a given environment facilitating bacterial adaptation. In this article current knowledge regarding plasmids resident in the human gut mobile metagenome is reviewed, and available strategies to access and characterize this portion of the gut microbiome are described. The relative merits of these methods and their present as well as prospective impact on our understanding of the human gut microbiota is discussed.","PeriodicalId":89091,"journal":{"name":"Bioengineered bugs","volume":"3 1","pages":"13-31"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/6b/f4/bbug-3-13.PMC3329251.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30290857","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

CDPK-driven changes in the intracellular ROS level and plant secondary metabolism. cdpk驱动细胞内ROS水平和植物次生代谢的变化。

Bioengineered bugs Pub Date : 2011-11-01 DOI: 10.4161/bbug.2.6.16803

Victor P Bulgakov, Tatiana Y Gorpenchenko, Yuri N Shkryl, Galina N Veremeichik, Natalia P Mischenko, Tatiana V Avramenko, Sergey A Fedoreyev, Yuri N Zhuravlev

引用次数: 30