生物设计研究(英文)最新文献_第6页

Dawn of a New Era for Membrane Protein Design. 膜蛋白设计新时代的曙光。

生物设计研究(英文) Pub Date : 2022-04-15 eCollection Date: 2022-01-01 DOI: 10.34133/2022/9791435

Shahin Sowlati-Hashjin, Aanshi Gandhi, Michael Garton

引用次数: 4

Design of Protein Segments and Peptides for Binding to Protein Targets. 用于与蛋白质靶标结合的蛋白质片段和肽的设计。

生物设计研究(英文) Pub Date : 2022-04-15 eCollection Date: 2022-01-01 DOI: 10.34133/2022/9783197

Suchetana Gupta, Noora Azadvari, Parisa Hosseinzadeh

引用次数: 0

iGEM 2021: A Year in Review. iGEM 2021：回顾一年。

生物设计研究(英文) Pub Date : 2022-03-14 eCollection Date: 2022-01-01 DOI: 10.34133/2022/9794609

Hannah Moon

引用次数: 0

What Have We Learned from Design of Function in Large Proteins? 我们从大蛋白质的功能设计中学到了什么？

生物设计研究(英文) Pub Date : 2022-03-08 eCollection Date: 2022-01-01 DOI: 10.34133/2022/9787581

Olga Khersonsky, Sarel J Fleishman

{"title":"What Have We Learned from Design of Function in Large Proteins?","authors":"Olga Khersonsky, Sarel J Fleishman","doi":"10.34133/2022/9787581","DOIUrl":"https://doi.org/10.34133/2022/9787581","url":null,"abstract":"The overarching goal of computational protein design is to gain complete control over protein structure and function. The majority of sophisticated binders and enzymes, however, are large and exhibit diverse and complex folds that defy atomistic design calculations. Encouragingly, recent strategies that combine evolutionary constraints from natural homologs with atomistic calculations have significantly improved design accuracy. In these approaches, evolutionary constraints mitigate the risk from misfolding and aggregation, focusing atomistic design calculations on a small but highly enriched sequence subspace. Such methods have dramatically optimized diverse proteins, including vaccine immunogens, enzymes for sustainable chemistry, and proteins with therapeutic potential. The new generation of deep learning-based ab initio structure predictors can be combined with these methods to extend the scope of protein design, in principle, to any natural protein of known sequence. We envision that protein engineering will come to rely on completely computational methods to efficiently discover and optimize biomolecular activities.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"2022 ","pages":"9787581"},"PeriodicalIF":0.0,"publicationDate":"2022-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241383","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: 4

Altered Carbon Partitioning Enhances CO₂ to Terpene Conversion in Cyanobacteria. 改变碳分配提高了蓝藻中CO2转化为萜烯的能力。

生物设计研究(英文) Pub Date : 2022-02-07 eCollection Date: 2022-01-01 DOI: 10.34133/2022/9897425

Man Li, Bin Long, Susie Y Dai, James W Golden, Xin Wang, Joshua S Yuan

{"title":"Altered Carbon Partitioning Enhances CO2 to Terpene Conversion in Cyanobacteria.","authors":"Man Li, Bin Long, Susie Y Dai, James W Golden, Xin Wang, Joshua S Yuan","doi":"10.34133/2022/9897425","DOIUrl":"10.34133/2022/9897425","url":null,"abstract":"Photosynthetic terpene production represents one of the most carbon and energy-efficient routes for converting CO2 into hydrocarbon. In photosynthetic organisms, metabolic engineering has led to limited success in enhancing terpene productivity, partially due to the low carbon partitioning. In this study, we employed systems biology analysis to reveal the strong competition for carbon substrates between primary metabolism (e.g., sucrose, glycogen, and protein synthesis) and terpene biosynthesis in Synechococcus elongatus PCC 7942. We then engineered key \"source\" and \"sink\" enzymes. The \"source\" limitation was overcome by knocking out either sucrose or glycogen biosynthesis to significantly enhance limonene production via altered carbon partitioning. Moreover, a fusion enzyme complex with geranyl diphosphate synthase (GPPS) and limonene synthase (LS) was designed to further improve pathway kinetics and substrate channeling. The synergy between \"source\" and \"sink\" achieved a limonene titer of 21.0 mg/L. Overall, the study demonstrates that balancing carbon flux between primary and secondary metabolism can be an effective approach to enhance terpene bioproduction in cyanobacteria. The design of \"source\" and \"sink\" synergy has significant potential in improving natural product yield in photosynthetic species.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"2022 ","pages":"9897425"},"PeriodicalIF":0.0,"publicationDate":"2022-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241349","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: 4

Making Use of Plant uORFs to Control Transgene Translation in Response to Pathogen Attack. 利用植物uORF控制转基因翻译以应对病原体攻击。

生物设计研究(英文) Pub Date : 2022-02-03 eCollection Date: 2022-01-01 DOI: 10.34133/2022/9820540

Gan Ai, Jin Liu, Xiaowei Fu, Tianli Li, Hai Zhu, Ying Zhai, Chuyan Xia, Weiye Pan, Jialu Li, Maofeng Jing, Danyu Shen, Ai Xia, Daolong Dou

{"title":"Making Use of Plant uORFs to Control Transgene Translation in Response to Pathogen Attack.","authors":"Gan Ai, Jin Liu, Xiaowei Fu, Tianli Li, Hai Zhu, Ying Zhai, Chuyan Xia, Weiye Pan, Jialu Li, Maofeng Jing, Danyu Shen, Ai Xia, Daolong Dou","doi":"10.34133/2022/9820540","DOIUrl":"10.34133/2022/9820540","url":null,"abstract":"Reducing crop loss to diseases is urgently needed to meet increasing food production challenges caused by the expanding world population and the negative impact of climate change on crop productivity. Disease-resistant crops can be created by expressing endogenous or exogenous genes of interest through transgenic technology. Nevertheless, enhanced resistance by overexpressing resistance-produced genes often results in adverse developmental affects. Upstream open reading frames (uORFs) are translational control elements located in the 5<math><msup><mrow></mrow><mrow><mo>'</mo></mrow></msup></math> untranslated region (UTR) of eukaryotic mRNAs and may repress the translation of downstream genes. To investigate the function of three uORFs from the 5<math><msup><mrow></mrow><mrow><mo>'</mo></mrow></msup></math>-UTR of ACCELERATED CELL 11 (uORFsACD11), we develop a fluorescent reporter system and find uORFsACD11 function in repressing downstream gene translation. Individual or simultaneous mutations of the three uORFsACD11 lead to repression of downstream translation efficiency at different levels. Importantly, uORFsACD11-mediated translational inhibition is impaired upon recognition of pathogen attack of plant leaves. When coupled with the PATHOGENESIS-RELATED GENE 1 (PR1) promoter, the uORFsACD11 cassettes can upregulate accumulation of Arabidopsis thaliana LECTIN RECEPTOR KINASE-VI.2 (AtLecRK-VI.2) during pathogen attack and enhance plant resistance to Phytophthora capsici. These findings indicate that the uORFsACD11 cassettes can be a useful toolkit that enables a high level of protein expression during pathogen attack, while for ensuring lower levels of protein expression at normal conditions.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"2022 ","pages":"9820540"},"PeriodicalIF":0.0,"publicationDate":"2022-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521741/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241374","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

Biological Parts for Engineering Abiotic Stress Tolerance in Plants. 工程植物非生物胁迫耐受的生物部件。

生物设计研究(英文) Pub Date : 2022-01-21 eCollection Date: 2022-01-01 DOI: 10.34133/2022/9819314

Neeta Lohani, Mohan B Singh, Prem L Bhalla

{"title":"Biological Parts for Engineering Abiotic Stress Tolerance in Plants.","authors":"Neeta Lohani, Mohan B Singh, Prem L Bhalla","doi":"10.34133/2022/9819314","DOIUrl":"https://doi.org/10.34133/2022/9819314","url":null,"abstract":"It is vital to ramp up crop production dramatically by 2050 due to the increasing global population and demand for food. However, with the climate change projections showing that droughts and heatwaves becoming common in much of the globe, there is a severe threat of a sharp decline in crop yields. Thus, developing crop varieties with inbuilt genetic tolerance to environmental stresses is urgently needed. Selective breeding based on genetic diversity is not keeping up with the growing demand for food and feed. However, the emergence of contemporary plant genetic engineering, genome-editing, and synthetic biology offer precise tools for developing crops that can sustain productivity under stress conditions. Here, we summarize the systems biology-level understanding of regulatory pathways involved in perception, signalling, and protective processes activated in response to unfavourable environmental conditions. The potential role of noncoding RNAs in the regulation of abiotic stress responses has also been highlighted. Further, examples of imparting abiotic stress tolerance by genetic engineering are discussed. Additionally, we provide perspectives on the rational design of abiotic stress tolerance through synthetic biology and list various bioparts that can be used to design synthetic gene circuits whose stress-protective functions can be switched on/off in response to environmental cues.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"2022 ","pages":"9819314"},"PeriodicalIF":0.0,"publicationDate":"2022-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521667/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241353","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: 16

De Novo Biosynthesis of Vindoline and Catharanthine in Saccharomyces cerevisiae 酿酒酵母中Vindoline和Catharanthine的De Novo生物合成

生物设计研究(英文) Pub Date : 2022-01-01 DOI: 10.34133/bdr.0002

Di Gao, Tengfei Liu, Jucan Gao, Junhao Xu, Yuanwei Gou, Yingjia Pan, Dongfang Li, Cuifang Ye, R. Pan, Lei Huang, Zhinan Xu, J. Lian

{"title":"De Novo Biosynthesis of Vindoline and Catharanthine in\u0000 Saccharomyces cerevisiae","authors":"Di Gao, Tengfei Liu, Jucan Gao, Junhao Xu, Yuanwei Gou, Yingjia Pan, Dongfang Li, Cuifang Ye, R. Pan, Lei Huang, Zhinan Xu, J. Lian","doi":"10.34133/bdr.0002","DOIUrl":"https://doi.org/10.34133/bdr.0002","url":null,"abstract":"\u0000 Vinblastine has been used clinically as one of the most potent therapeutics for the treatment of several types of cancer. However, the traditional plant extraction method suffers from unreliable supply, low abundance, and extremely high cost. Here, we use synthetic biology approach to engineer\u0000 Saccharomyces cerevisiae\u0000 for de novo biosynthesis of vindoline and catharanthine, which can be coupled chemically or biologically to vinblastine. On the basis of a platform strain with sufficient supply of precursors and cofactors for biosynthesis, we reconstituted, debottlenecked, and optimized the biosynthetic pathways for the production of vindoline and catharanthine. The vindoline biosynthetic pathway represents one of the most complicated pathways ever reconstituted in microbial cell factories. Using shake flask fermentation, our engineered yeast strains were able to produce catharanthine and vindoline at a titer of 527.1 and 305.1 μg·liter\u0000 −1\u0000 , respectively, without accumulating detectable amount of pathway intermediates. This study establishes a representative example for the production of valuable plant natural products in yeast.\u0000","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49294496","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: 4

Tissue Regeneration with Hydrogel Encapsulation: A Review of Developments in Plants and Animals. 水凝胶包埋组织再生：植物和动物研究进展综述。

生物设计研究(英文) Pub Date : 2021-12-02 eCollection Date: 2021-01-01 DOI: 10.34133/2021/9890319

Srikumar Krishnamoorthy, Michael F Schwartz, Lisa Van den Broeck, Aitch Hunt, Timothy J Horn, Rosangela Sozzani

引用次数: 0

Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal. 用于植物生物设计的生物部件，以增强陆地二氧化碳去除。

生物设计研究(英文) Pub Date : 2021-11-29 eCollection Date: 2021-01-01 DOI: 10.34133/2021/9798714

Xiaohan Yang, Degao Liu, Haiwei Lu, David J Weston, Jin-Gui Chen, Wellington Muchero, Stanton Martin, Yang Liu, Md Mahmudul Hassan, Guoliang Yuan, Udaya C Kalluri, Timothy J Tschaplinski, Julie C Mitchell, Stan D Wullschleger, Gerald A Tuskan

{"title":"Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal.","authors":"Xiaohan Yang, Degao Liu, Haiwei Lu, David J Weston, Jin-Gui Chen, Wellington Muchero, Stanton Martin, Yang Liu, Md Mahmudul Hassan, Guoliang Yuan, Udaya C Kalluri, Timothy J Tschaplinski, Julie C Mitchell, Stan D Wullschleger, Gerald A Tuskan","doi":"10.34133/2021/9798714","DOIUrl":"10.34133/2021/9798714","url":null,"abstract":"A grand challenge facing society is climate change caused mainly by rising CO2 concentration in Earth's atmosphere. Terrestrial plants are linchpins in global carbon cycling, with a unique capability of capturing CO2 via photosynthesis and translocating captured carbon to stems, roots, and soils for long-term storage. However, many researchers postulate that existing land plants cannot meet the ambitious requirement for CO2 removal to mitigate climate change in the future due to low photosynthetic efficiency, limited carbon allocation for long-term storage, and low suitability for the bioeconomy. To address these limitations, there is an urgent need for genetic improvement of existing plants or construction of novel plant systems through biosystems design (or biodesign). Here, we summarize validated biological parts (e.g., protein-encoding genes and noncoding RNAs) for biological engineering of carbon dioxide removal (CDR) traits in terrestrial plants to accelerate land-based decarbonization in bioenergy plantations and agricultural settings and promote a vibrant bioeconomy. Specifically, we first summarize the framework of plant-based CDR (e.g., CO2 capture, translocation, storage, and conversion to value-added products). Then, we highlight some representative biological parts, with experimental evidence, in this framework. Finally, we discuss challenges and strategies for the identification and curation of biological parts for CDR engineering in plants.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"2021 ","pages":"9798714"},"PeriodicalIF":0.0,"publicationDate":"2021-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241338","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