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Engineering highly productive cyanobacteria towards carbon negative emissions technologies 利用高产蓝藻工程技术实现碳负排技术
IF 7.7 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-05-11 DOI: 10.1016/j.copbio.2024.103141
Angelo J Victoria , Michael J Astbury , Alistair J McCormick
{"title":"Engineering highly productive cyanobacteria towards carbon negative emissions technologies","authors":"Angelo J Victoria ,&nbsp;Michael J Astbury ,&nbsp;Alistair J McCormick","doi":"10.1016/j.copbio.2024.103141","DOIUrl":"https://doi.org/10.1016/j.copbio.2024.103141","url":null,"abstract":"<div><p>Cyanobacteria are a diverse and ecologically important group of photosynthetic prokaryotes that contribute significantly to the global carbon cycle through the capture of CO<sub>2</sub> as biomass. Cyanobacterial biotechnology could play a key role in a sustainable bioeconomy through negative emissions technologies (NETs), such as carbon sequestration or bioproduction. However, the primary issues of low productivities and high infrastructure costs currently limit the commercialisation of such applications. The isolation of several fast-growing strains and recent advancements in molecular biology tools now offer promising new avenues for improving yields, including metabolic engineering approaches guided by high-throughput screening and metabolic models. Furthermore, emerging research on engineering coculture communities could help to develop more robust culturing systems to support broader NET applications.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"87 ","pages":"Article 103141"},"PeriodicalIF":7.7,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0958166924000776/pdfft?md5=8f561c6a8223113a95b21e071bdfc231&pid=1-s2.0-S0958166924000776-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140906834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Unlocking plant bioactive pathways: omics data harnessing and machine learning assisting 揭示植物生物活性途径：omics 数据利用和机器学习辅助
IF 7.7 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-05-09 DOI: 10.1016/j.copbio.2024.103135
Mickael Durand , Sébastien Besseau , Nicolas Papon , Vincent Courdavault
{"title":"Unlocking plant bioactive pathways: omics data harnessing and machine learning assisting","authors":"Mickael Durand ,&nbsp;Sébastien Besseau ,&nbsp;Nicolas Papon ,&nbsp;Vincent Courdavault","doi":"10.1016/j.copbio.2024.103135","DOIUrl":"https://doi.org/10.1016/j.copbio.2024.103135","url":null,"abstract":"<div><p>Plant bioactives hold immense potential in the medicine and food industry. The recent advancements in omics applied in deciphering specialized metabolic pathways underscore the importance of high-quality genome releases and the wealth of data in metabolomics and transcriptomics. While harnessing data, whether integrated or standalone, has proven successful in unveiling plant natural product (PNP) biosynthetic pathways, the democratization of machine learning in biology opens exciting new opportunities for enhancing the exploration of these pathways. This review highlights the recent breakthroughs in disrupting plant-specialized biosynthetic pathways through the utilization of omics data harnessing and machine learning techniques.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"87 ","pages":"Article 103135"},"PeriodicalIF":7.7,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0958166924000715/pdfft?md5=faeb460050cd7f736cb0e9555fd8e875&pid=1-s2.0-S0958166924000715-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140894333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Technologies for the discovery of G protein–coupled receptor–targeting biologics 发现 G 蛋白偶联受体靶向生物制剂的技术
IF 7.7 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-05-09 DOI: 10.1016/j.copbio.2024.103138
McKenna L Downey , Pamela Peralta-Yahya
{"title":"Technologies for the discovery of G protein–coupled receptor–targeting biologics","authors":"McKenna L Downey ,&nbsp;Pamela Peralta-Yahya","doi":"10.1016/j.copbio.2024.103138","DOIUrl":"https://doi.org/10.1016/j.copbio.2024.103138","url":null,"abstract":"<div><p>G protein–coupled receptors (GPCRs) are important pharmaceutical targets, working as entry points for signaling pathways involved in metabolic, neurological, and cardiovascular diseases. Although small molecules remain the major GPCR drug type, biologic therapeutics, such as peptides and antibodies, are increasingly found among clinical trials and Food and Drug Administration (FDA)-approved drugs. Here, we review state-of-the-art technologies for the engineering of biologics that target GPCRs, as well as proof-of-principle technologies that are ripe for this application. Looking ahead, inexpensive DNA synthesis will enable the routine generation of computationally predesigned libraries for use in display assays for the rapid discovery of GPCR binders. Advances in synthetic biology are enabling the increased throughput of functional GPCR assays to the point that they can be used to directly identify biologics that modulate GPCR activity. Finally, we give an overview of adjacent technologies that are ripe for application to discover biologics that target human GPCRs.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"87 ","pages":"Article 103138"},"PeriodicalIF":7.7,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140901888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sourcing DNA parts for synthetic biology applications in plants 为植物合成生物学应用寻找 DNA 部件
IF 7.7 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-05-08 DOI: 10.1016/j.copbio.2024.103140
Katie Vollen , Chengsong Zhao , Jose M Alonso, Anna N Stepanova
{"title":"Sourcing DNA parts for synthetic biology applications in plants","authors":"Katie Vollen ,&nbsp;Chengsong Zhao ,&nbsp;Jose M Alonso,&nbsp;Anna N Stepanova","doi":"10.1016/j.copbio.2024.103140","DOIUrl":"https://doi.org/10.1016/j.copbio.2024.103140","url":null,"abstract":"<div><p>Transgenic approaches are now standard in plant biology research aiming to characterize gene function or improve crops. Recent advances in DNA synthesis and assembly make constructing transgenes a routine task. What remains nontrivial is the selection of the DNA parts and optimization of the transgene design. Early career researchers and seasoned molecular biologists alike often face difficult decisions on what promoter or terminator to use, what tag to include, and where to place it. This review aims to inform about the current approaches being employed to identify and characterize DNA parts with the desired functionalities and give general advice on basic construct design. Furthermore, we hope to share the excitement about new experimental and computational tools being developed in this field.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"87 ","pages":"Article 103140"},"PeriodicalIF":7.7,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140893249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Phytosensors: harnessing plants to understand the world around us 植物传感器：利用植物了解我们周围的世界
IF 7.7 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-05-04 DOI: 10.1016/j.copbio.2024.103134
Alexander C Pfotenhauer , Scott C Lenaghan
{"title":"Phytosensors: harnessing plants to understand the world around us","authors":"Alexander C Pfotenhauer ,&nbsp;Scott C Lenaghan","doi":"10.1016/j.copbio.2024.103134","DOIUrl":"https://doi.org/10.1016/j.copbio.2024.103134","url":null,"abstract":"<div><p>Although plants are sessile, their ubiquitous distribution, ability to harness energy from the sun, and ability to sense above and belowground signals make them ideal candidates for biosensor development. Synthetic biology has allowed scientists to reimagine biosensors as engineered devices that are focused on accomplishing novel tasks. As such, a new wave of plant-based sensors, phytosensors, are being engineered as multi-component sense-and-report devices that can alert human operators to a variety of hazards. While phytosensors are intrinsically tied to agriculture, a new generation of phytosensors has been envisioned to function in the built environment and even in austere environments, such as space. In this review, we will explore the current state of the art with regard to phytosensor engineering.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"87 ","pages":"Article 103134"},"PeriodicalIF":7.7,"publicationDate":"2024-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140824102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reconstitution and optimization of complex plant natural product biosynthetic pathways in microbial expression systems 在微生物表达系统中重建和优化复杂的植物天然产物生物合成途径
IF 7.7 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-05-04 DOI: 10.1016/j.copbio.2024.103136
Jucan Gao , Yuanwei Gou , Lei Huang , Jiazhang Lian
{"title":"Reconstitution and optimization of complex plant natural product biosynthetic pathways in microbial expression systems","authors":"Jucan Gao ,&nbsp;Yuanwei Gou ,&nbsp;Lei Huang ,&nbsp;Jiazhang Lian","doi":"10.1016/j.copbio.2024.103136","DOIUrl":"https://doi.org/10.1016/j.copbio.2024.103136","url":null,"abstract":"<div><p>Plant natural products (PNPs) are a diverse group of chemical compounds synthesized by plants for various biological purposes and play a significant role in the fields of medicine, agriculture, and industry. In recent years, the development of synthetic biology promises the production of PNPs in microbial expression systems in a sustainable, low-cost, and large-scale manner. This review first introduces multiplex genome editing and PNP pathway assembly in microbial expression systems. Then recent technologies and examples geared toward improving PNP biosynthetic efficiency are discussed from three aspects: pathway optimization, chassis optimization, and modular coculture engineering. Finally, the review is concluded with future perspectives on the combination of machine learning and BioFoundry for the reconstitution and optimization of PNP microbial cell factories.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"87 ","pages":"Article 103136"},"PeriodicalIF":7.7,"publicationDate":"2024-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140824101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Building Synthetic Yeast Factories to Produce Fat-soluble Antioxidants 建造合成酵母工厂生产脂溶性抗氧化剂
IF 7.7 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-05-03 DOI: 10.1016/j.copbio.2024.103129
Yuxin Zhao , Zhanyi Yao , Vedika Desai , Dan Chen , Zengyi Shao
{"title":"Building Synthetic Yeast Factories to Produce Fat-soluble Antioxidants","authors":"Yuxin Zhao ,&nbsp;Zhanyi Yao ,&nbsp;Vedika Desai ,&nbsp;Dan Chen ,&nbsp;Zengyi Shao","doi":"10.1016/j.copbio.2024.103129","DOIUrl":"https://doi.org/10.1016/j.copbio.2024.103129","url":null,"abstract":"<div><p>Fat-soluble antioxidants play a vital role in protecting the body against oxidative stress and damage. The rapid advancements in metabolic engineering and synthetic biology have offered a promising avenue for economically producing fat-soluble antioxidants by engineering microbial chassis. This review provides an overview of the recent progress in engineering yeast microbial factories to produce three main groups of lipophilic antioxidants: carotenoids, vitamin E, and stilbenoids. In addition to discussing the classic strategies employed to improve precursor availability and alleviate carbon flux competition, this review delves deeper into the innovative approaches focusing on enzyme engineering, product sequestration, subcellular compartmentalization, multistage fermentation, and morphology engineering. We conclude the review by highlighting the prospects of microbial engineering for lipophilic antioxidant production.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"87 ","pages":"Article 103129"},"PeriodicalIF":7.7,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140820147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthetic reprogramming of plant developmental and biochemical pathways 植物发育和生化途径的合成重编程
IF 7.7 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-04-30 DOI: 10.1016/j.copbio.2024.103139
Shammi Akter , Oscar Castaneda-Méndez , Jesús Beltrán
{"title":"Synthetic reprogramming of plant developmental and biochemical pathways","authors":"Shammi Akter ,&nbsp;Oscar Castaneda-Méndez ,&nbsp;Jesús Beltrán","doi":"10.1016/j.copbio.2024.103139","DOIUrl":"https://doi.org/10.1016/j.copbio.2024.103139","url":null,"abstract":"<div><p>Plant synthetic biology (Plant SynBio) is an emerging field with the potential to enhance agriculture, human health, and sustainability. Integrating genetic tools and engineering principles, Plant SynBio aims to manipulate cellular functions and construct novel biochemical pathways to develop plants with new phenotypic traits, enhanced yield, and be able to produce natural products and pharmaceuticals. This review compiles research efforts in reprogramming plant developmental and biochemical pathways. We highlight studies leveraging new gene expression toolkits to alter plant architecture for improved performance in model and crop systems and to produce useful metabolites in plant tissues. Furthermore, we provide insights into the challenges and opportunities associated with the adoption of Plant SynBio in addressing complex issues impacting agriculture and human health.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"87 ","pages":"Article 103139"},"PeriodicalIF":7.7,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140813151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
‘From metabolism to metabolism’: holistic considerations on B-vitamin interactions, biofortification, and deficiencies 从新陈代谢到新陈代谢"：对 B 族维生素相互作用、生物强化和缺乏症的整体考虑
IF 7.7 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-04-26 DOI: 10.1016/j.copbio.2024.103132
Lisa De Zanetti, Dominique Van Der Straeten
{"title":"‘From metabolism to metabolism’: holistic considerations on B-vitamin interactions, biofortification, and deficiencies","authors":"Lisa De Zanetti,&nbsp;Dominique Van Der Straeten","doi":"10.1016/j.copbio.2024.103132","DOIUrl":"https://doi.org/10.1016/j.copbio.2024.103132","url":null,"abstract":"<div><p>In the post-Green Revolution era, disparities in dietary access, rising obesity rates, demographic shifts, adoption of plant-based diets, and the impact of climate change collectively contribute to a progressive decline in dietary nutritional value, exacerbating B vitamin deficiencies across both low- and high-income countries. While the prevailing focus of biofortification has been on three micronutrients — provitamin A, iron, and zinc — utilizing conventional breeding, it is imperative to diversify biofortification strategies to combat micronutrient malnutrition. Metabolic engineering, facilitated by biotechnological tools, presents a promising avenue, contingent upon advances in fundamental knowledge, technological innovation, regulatory updates, and sustained public funding. Recognizing the intricate metabolic interplay of B vitamins in plants and humans, a comprehensive ‘from metabolism to metabolism’ approach is crucial for designing effective biofortification strategies that target multiple vitamins. This holistic perspective also extends beyond individual crops to encompass the entire food chain, a complex socioeconomic ecosystem that necessitates a paradigm shift, prioritizing quality over quantity.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"87 ","pages":"Article 103132"},"PeriodicalIF":7.7,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0958166924000685/pdfft?md5=1adcb29f315e052b4d91764840cc5532&pid=1-s2.0-S0958166924000685-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140646767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cutting-edge plant natural product pathway elucidation 前沿植物天然产物途径阐释
IF 7.7 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-04-26 DOI: 10.1016/j.copbio.2024.103137
Jianing Han , Emma Parker Miller , Sijin Li
{"title":"Cutting-edge plant natural product pathway elucidation","authors":"Jianing Han ,&nbsp;Emma Parker Miller ,&nbsp;Sijin Li","doi":"10.1016/j.copbio.2024.103137","DOIUrl":"https://doi.org/10.1016/j.copbio.2024.103137","url":null,"abstract":"<div><p>Plant natural products (PNPs) play important roles in plant physiology and have been applied across diverse fields of human society. Understanding their biosynthetic pathways informs plant evolution and meanwhile enables sustainable production through metabolic engineering. However, the discovery of PNP biosynthetic pathways remains challenging due to the diversity of enzymes involved and limitations in traditional gene mining approaches. In this review, we will summarize state-of-the-art strategies and recent examples for predicting and characterizing PNP biosynthetic pathways, respectively, with multiomics-guided tools and heterologous host systems and share our perspectives on the systematic pipelines integrating these various bioinformatic and biochemical approaches.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"87 ","pages":"Article 103137"},"PeriodicalIF":7.7,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140650817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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