Wentao Zheng , Yandong Xia , Xue Wang , Shiqing Gao , Diao Zhou , Jun Fu , Ruijuan Li , Jia Yin
{"title":"Cascade-Cas3 facilitates high-accuracy genome engineering in Pseudomonas using phage-encoded homologous recombination","authors":"Wentao Zheng , Yandong Xia , Xue Wang , Shiqing Gao , Diao Zhou , Jun Fu , Ruijuan Li , Jia Yin","doi":"10.1016/j.engmic.2022.100046","DOIUrl":"https://doi.org/10.1016/j.engmic.2022.100046","url":null,"abstract":"<div><p>Phage-encoded homologous recombination (PEHR) is an efficient tool for bacterial genome editing. We previously developed and utilized a <em>Pseudomonas</em>-specific PEHR system. However, when using the PEHR system for <em>Pseudomonas</em> genome editing, false positives can be a problem. In this study, we combined a compact Cascade-Cas3 system from <em>P. aeruginosa</em> (PaeCas3c) with a <em>Pseudomonas</em>-specific PEHR system, and the results of our recombineering assay showed that this compact Cascade-Cas3 system can significantly improve PEHR recombineering accuracy.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"2 4","pages":"Article 100046"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370322000376/pdfft?md5=a12b787c80196df3398b31290dd7b8bb&pid=1-s2.0-S2667370322000376-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71894966","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}
{"title":"Recent developments in the identification and biosynthesis of antitumor drugs derived from microorganisms","authors":"Qi Gao , Sizhe Deng , Tianyu Jiang","doi":"10.1016/j.engmic.2022.100047","DOIUrl":"https://doi.org/10.1016/j.engmic.2022.100047","url":null,"abstract":"<div><p>Secondary metabolites in microorganisms represent a resource for drug discovery and development. In particular, microbial-derived antitumor agents are in clinical use worldwide. Herein, we provide an overview of the development of classical antitumor drugs derived from microorganisms. Currently used drugs and drug candidates are comprehensively described in terms of pharmacological activities, mechanisms of action, microbial sources, and biosynthesis. We further discuss recent studies that have demonstrated the utility of gene-editing technologies and synthetic biology tools for the identification of new gene clusters, expansion of natural products, and elucidation of biosynthetic pathways. This review summarizes recent progress in the discovery and development of microbial-derived anticancer compounds with emphasis on biosynthesis.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"2 4","pages":"Article 100047"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370322000388/pdfft?md5=0d96e2e750864f94da9230fc075e2fdb&pid=1-s2.0-S2667370322000388-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71894962","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}
John N. Idenyi , Jonathan C. Eya , Amechi S. Nwankwegu , Emeka G. Nwoba
{"title":"Aquaculture sustainability through alternative dietary ingredients: Microalgal value-added products","authors":"John N. Idenyi , Jonathan C. Eya , Amechi S. Nwankwegu , Emeka G. Nwoba","doi":"10.1016/j.engmic.2022.100049","DOIUrl":"https://doi.org/10.1016/j.engmic.2022.100049","url":null,"abstract":"<div><p>Aquaculture contributes remarkably to the global economy and food security through seafood production, an important part of the global food supply chain. The success of this industry depends heavily on aquafeeds, and the nutritional composition of the feed is an important factor for the quality, productivity, and profitability of aquaculture species. The sustainability of the aquaculture industry depends on the accessibility of quality feed ingredients, such as fishmeal and fish oil. These traditional feedstuffs are under increasing significant pressure due to the rapid expansion of aquaculture for human consumption and the decline of natural fish harvest. In this review, we evaluated the development of microalgal molecules in aquaculture and expanded the use of these high-value compounds in the production of aquaculture diets. Microalgae-derived functional ingredients emerged as one of the promising alternatives for aquafeed production with positive health benefits. Several compounds found in microalgae, including carotenoids (lutein, astaxanthin, and β-carotene), essential amino acids (leucine, valine, and threonine), β-1–3-glucan, essential oils (docosahexaenoic acid and eicosapentaenoic acid), minerals, and vitamins, are of high nutritional value to aquaculture.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"2 4","pages":"Article 100049"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370322000406/pdfft?md5=06265d972f4fa1627cbf4a7604ac81c7&pid=1-s2.0-S2667370322000406-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71894967","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}
Engineering MicrobiologyPub Date : 2022-10-01eCollection Date: 2022-12-01DOI: 10.1016/j.engmic.2022.100050
Jianping Huang, Shengxiong Huang
{"title":"Bioproduction of monoterpene indole alkaloids in a single cell factory.","authors":"Jianping Huang, Shengxiong Huang","doi":"10.1016/j.engmic.2022.100050","DOIUrl":"10.1016/j.engmic.2022.100050","url":null,"abstract":"<p><p>The <i>de novo</i> biosynthesis of vindoline and catharanthine, the direct precursors used for industrial production of the anti-cancer drug vinblastine, has been achieved in the yeast cell factory. To date, this is the longest natural product biosynthesis pathway that has been successfully transferred from plants to microorganisms, indicating the possibility of producing more than 3,000 other monoterpene indole alkaloids in yeast by synthetic genome engineering.</p>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"15 12","pages":"100050"},"PeriodicalIF":0.0,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91421065","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}
Engineering MicrobiologyPub Date : 2022-09-21eCollection Date: 2022-12-01DOI: 10.1016/j.engmic.2022.100049
John N Idenyi, Jonathan C Eya, Amechi S Nwankwegu, Emeka G Nwoba
{"title":"Aquaculture sustainability through alternative dietary ingredients: Microalgal value-added products.","authors":"John N Idenyi, Jonathan C Eya, Amechi S Nwankwegu, Emeka G Nwoba","doi":"10.1016/j.engmic.2022.100049","DOIUrl":"10.1016/j.engmic.2022.100049","url":null,"abstract":"<p><p>Aquaculture contributes remarkably to the global economy and food security through seafood production, an important part of the global food supply chain. The success of this industry depends heavily on aquafeeds, and the nutritional composition of the feed is an important factor for the quality, productivity, and profitability of aquaculture species. The sustainability of the aquaculture industry depends on the accessibility of quality feed ingredients, such as fishmeal and fish oil. These traditional feedstuffs are under increasing significant pressure due to the rapid expansion of aquaculture for human consumption and the decline of natural fish harvest. In this review, we evaluated the development of microalgal molecules in aquaculture and expanded the use of these high-value compounds in the production of aquaculture diets. Microalgae-derived functional ingredients emerged as one of the promising alternatives for aquafeed production with positive health benefits. Several compounds found in microalgae, including carotenoids (lutein, astaxanthin, and β-carotene), essential amino acids (leucine, valine, and threonine), β-1-3-glucan, essential oils (docosahexaenoic acid and eicosapentaenoic acid), minerals, and vitamins, are of high nutritional value to aquaculture.</p>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"35 1","pages":"100049"},"PeriodicalIF":0.0,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611001/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77100512","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}
Engineering MicrobiologyPub Date : 2022-09-12eCollection Date: 2022-12-01DOI: 10.1016/j.engmic.2022.100048
Dake Liu, Nicole E Siguenza, Amir Zarrinpar, Yousong Ding
{"title":"Methods of DNA introduction for the engineering of commensal microbes.","authors":"Dake Liu, Nicole E Siguenza, Amir Zarrinpar, Yousong Ding","doi":"10.1016/j.engmic.2022.100048","DOIUrl":"10.1016/j.engmic.2022.100048","url":null,"abstract":"<p><p>The microbiome is an essential component of ecological systems and is comprised of a diverse array of microbes. Over the past decades, the accumulated observational evidence reveals a close correlation between the microbiome and human health and disease. Many groups are now manipulating individual microbial strains, species and the community as a whole to gain a mechanistic understanding of the functions of the microbiome. Here, we discuss three major approaches for introducing DNA to engineer model bacteria and isolated undomesticated bacteria, including transformation, transduction, and conjugation. We provide an overview of these approaches and describe the advantages and limitations of each method. In addition, we highlight examples of human microbiome engineering using these approaches. Finally, we provide perspectives for the future of microbiome engineering.</p>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"1 1","pages":"100048"},"PeriodicalIF":0.0,"publicationDate":"2022-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610962/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89698005","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}
Engineering MicrobiologyPub Date : 2022-09-03eCollection Date: 2022-12-01DOI: 10.1016/j.engmic.2022.100047
Qi Gao, Sizhe Deng, Tianyu Jiang
{"title":"Recent developments in the identification and biosynthesis of antitumor drugs derived from microorganisms.","authors":"Qi Gao, Sizhe Deng, Tianyu Jiang","doi":"10.1016/j.engmic.2022.100047","DOIUrl":"10.1016/j.engmic.2022.100047","url":null,"abstract":"<p><p>Secondary metabolites in microorganisms represent a resource for drug discovery and development. In particular, microbial-derived antitumor agents are in clinical use worldwide. Herein, we provide an overview of the development of classical antitumor drugs derived from microorganisms. Currently used drugs and drug candidates are comprehensively described in terms of pharmacological activities, mechanisms of action, microbial sources, and biosynthesis. We further discuss recent studies that have demonstrated the utility of gene-editing technologies and synthetic biology tools for the identification of new gene clusters, expansion of natural products, and elucidation of biosynthetic pathways. This review summarizes recent progress in the discovery and development of microbial-derived anticancer compounds with emphasis on biosynthesis.</p>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"25 1","pages":"100047"},"PeriodicalIF":0.0,"publicationDate":"2022-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611020/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81738074","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}
Wenxia Song, Xueke Zhuang, Yahong Tan, Qingsheng Qi, Xuemei Lu
{"title":"The type IX secretion system: Insights into its function and connection to glycosylation in Cytophaga hutchinsonii","authors":"Wenxia Song, Xueke Zhuang, Yahong Tan, Qingsheng Qi, Xuemei Lu","doi":"10.1016/j.engmic.2022.100038","DOIUrl":"https://doi.org/10.1016/j.engmic.2022.100038","url":null,"abstract":"<div><p>The recently discovered type IX secretion system (T9SS) is limited to the Bacteroidetes phylum. <em>Cytophaga hutchinsonii</em>, a member of the Bacteroidetes phylum widely spread in soil, has complete orthologs of T9SS components and many T9SS substrates. <em>C. hutchinsonii</em> can efficiently degrade crystalline cellulose using a novel strategy, in which bacterial cells must be in direct contact with cellulose. It can rapidly glide over surfaces via unclear mechanisms. Studies have shown that T9SS plays an important role in cellulose degradation, gliding motility, and ion assimilation in <em>C. hutchinsonii</em>. As reported recently, T9SS substrates are <em>N</em>- or <em>O</em>-glycosylated at their C-terminal domains (CTDs), with <em>N</em>-glycosylation being related to the translocation and outer membrane anchoring of these proteins. These findings have deepened our understanding of T9SS in <em>C. hutchinsonii</em>. In this review, we focused on the research progress on diverse substrates and functions of T9SS in <em>C. hutchinsonii</em> and the glycosylation of its substrates. A model of T9SS functions and the glycosylation of its substrates was proposed.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"2 3","pages":"Article 100038"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370322000297/pdfft?md5=434ec9b499cefc5eb233b60b01f5e3ca&pid=1-s2.0-S2667370322000297-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71901146","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}
{"title":"Discovery and analysis of a new class of triterpenes derived from hexaprenyl pyrophosphate","authors":"Dan Hu","doi":"10.1016/j.engmic.2022.100035","DOIUrl":"https://doi.org/10.1016/j.engmic.2022.100035","url":null,"abstract":"<div><p>Triterpenes are derived from squalene or oxidosqualene. However, a new class of triterpenes derived from hexaprenyl pyrophosphate has been recently discovered, formed by a new family of chimeric class I triterpene synthases. The cyclization mechanisms of triterpenes were elucidated by isotopic labeling and protein structural analyses, which helps understand the biosynthesis of triterpenes in nature.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"2 3","pages":"Article 100035"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370322000261/pdfft?md5=c826781e7a1fc24a2cab8717beaca2ee&pid=1-s2.0-S2667370322000261-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71900307","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}
Xuewen Hou , Ruonan Sun , Yanyan Feng , Runfang Zhang , Tianjiao Zhu , Qian Che , Guojian Zhang , Dehai Li
{"title":"Peptaibols: Diversity, bioactivity, and biosynthesis","authors":"Xuewen Hou , Ruonan Sun , Yanyan Feng , Runfang Zhang , Tianjiao Zhu , Qian Che , Guojian Zhang , Dehai Li","doi":"10.1016/j.engmic.2022.100026","DOIUrl":"https://doi.org/10.1016/j.engmic.2022.100026","url":null,"abstract":"<div><p>Peptaibols are a large family of linear, amphipathic polypeptides consisting of 5-20 amino acid residues generated from the fungal nonribosomal peptide synthetase (NRPS) pathway. With a relatively high content of non-proteinogenic amino acids such as <em>α</em>-aminoisobutyrate (Aib) and isovaline (Iva) in the skeleton, peptaibols exhibit a wide range of biological activities, including anti-microbial, cytotoxic, and neuroleptic effects. With five peptaibols brought to market for use as biocontrol agents, this class of peptides has received increasing attention from both biochemists and pharmacologists. In this review, we summarized the progress made in structural characterization, elucidation of biosynthetic pathways, and investigation of biosynthesis elucidation and bioactivities, to promote further efforts to develop peptaibols as pharmaceuticals.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"2 3","pages":"Article 100026"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370322000170/pdfft?md5=6089e83b083385bbf9baf891b2a9e28e&pid=1-s2.0-S2667370322000170-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71901150","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}