Pengjie Yang , Jinzhong Tian , Lu Zhang , Hui Zhang , Gaohua Yang , Yimeng Ren , Jingyuan Fang , Yang Gu , Weihong Jiang
{"title":"肠道共生梭菌遗传操作工具箱","authors":"Pengjie Yang , Jinzhong Tian , Lu Zhang , Hui Zhang , Gaohua Yang , Yimeng Ren , Jingyuan Fang , Yang Gu , Weihong Jiang","doi":"10.1016/j.synbio.2023.12.005","DOIUrl":null,"url":null,"abstract":"<div><p>Gut microbes are closely related with human health, but remain much to learn. <em>Clostridium symbiosum</em> is a conditionally pathogenic human gut bacterium and regarded as a potential biomarker for early diagnosis of intestinal tumors. However, the absence of an efficient toolbox that allows diverse genetic manipulations of this bacterium limits its in-depth studies. Here, we obtained the complete genome sequence of <em>C. symbiosum</em> ATCC 14940, a representative strain of <em>C. symbiosum</em>. On this basis, we further developed a series of genetic manipulation methods for this bacterium. Firstly, following the identification of a functional replicon pBP1 in <em>C. symbiosum</em> ATCC 14940, a highly efficient conjugative DNA transfer method was established, enabling the rapid introduction of exogenous plasmids into cells. Next, we constructed a dual-plasmid CRISPR/Cas12a system for genome editing in this bacterium, reaching over 60 % repression for most of the chosen genes as well as efficient deletion (>90 %) of three target genes. Finally, this toolbox was used for the identification of crucial functional genes, involving growth, synthesis of important metabolites, and virulence of <em>C. symbiosum</em> ATCC 14940. Our work has effectively established and optimized genome editing methods in intestinal <em>C. symbiosum</em>, thereby providing strong support for further basic and application research in this bacterium.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.4000,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X23001126/pdfft?md5=4bbc1e472ee3d742a0ea74d0155338f8&pid=1-s2.0-S2405805X23001126-main.pdf","citationCount":"0","resultStr":"{\"title\":\"A toolbox for genetic manipulation in intestinal Clostridium symbiosum\",\"authors\":\"Pengjie Yang , Jinzhong Tian , Lu Zhang , Hui Zhang , Gaohua Yang , Yimeng Ren , Jingyuan Fang , Yang Gu , Weihong Jiang\",\"doi\":\"10.1016/j.synbio.2023.12.005\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Gut microbes are closely related with human health, but remain much to learn. <em>Clostridium symbiosum</em> is a conditionally pathogenic human gut bacterium and regarded as a potential biomarker for early diagnosis of intestinal tumors. However, the absence of an efficient toolbox that allows diverse genetic manipulations of this bacterium limits its in-depth studies. Here, we obtained the complete genome sequence of <em>C. symbiosum</em> ATCC 14940, a representative strain of <em>C. symbiosum</em>. On this basis, we further developed a series of genetic manipulation methods for this bacterium. Firstly, following the identification of a functional replicon pBP1 in <em>C. symbiosum</em> ATCC 14940, a highly efficient conjugative DNA transfer method was established, enabling the rapid introduction of exogenous plasmids into cells. Next, we constructed a dual-plasmid CRISPR/Cas12a system for genome editing in this bacterium, reaching over 60 % repression for most of the chosen genes as well as efficient deletion (>90 %) of three target genes. Finally, this toolbox was used for the identification of crucial functional genes, involving growth, synthesis of important metabolites, and virulence of <em>C. symbiosum</em> ATCC 14940. Our work has effectively established and optimized genome editing methods in intestinal <em>C. symbiosum</em>, thereby providing strong support for further basic and application research in this bacterium.</p></div>\",\"PeriodicalId\":22148,\"journal\":{\"name\":\"Synthetic and Systems Biotechnology\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":4.4000,\"publicationDate\":\"2023-12-29\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S2405805X23001126/pdfft?md5=4bbc1e472ee3d742a0ea74d0155338f8&pid=1-s2.0-S2405805X23001126-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Synthetic and Systems Biotechnology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2405805X23001126\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Synthetic and Systems Biotechnology","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2405805X23001126","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
A toolbox for genetic manipulation in intestinal Clostridium symbiosum
Gut microbes are closely related with human health, but remain much to learn. Clostridium symbiosum is a conditionally pathogenic human gut bacterium and regarded as a potential biomarker for early diagnosis of intestinal tumors. However, the absence of an efficient toolbox that allows diverse genetic manipulations of this bacterium limits its in-depth studies. Here, we obtained the complete genome sequence of C. symbiosum ATCC 14940, a representative strain of C. symbiosum. On this basis, we further developed a series of genetic manipulation methods for this bacterium. Firstly, following the identification of a functional replicon pBP1 in C. symbiosum ATCC 14940, a highly efficient conjugative DNA transfer method was established, enabling the rapid introduction of exogenous plasmids into cells. Next, we constructed a dual-plasmid CRISPR/Cas12a system for genome editing in this bacterium, reaching over 60 % repression for most of the chosen genes as well as efficient deletion (>90 %) of three target genes. Finally, this toolbox was used for the identification of crucial functional genes, involving growth, synthesis of important metabolites, and virulence of C. symbiosum ATCC 14940. Our work has effectively established and optimized genome editing methods in intestinal C. symbiosum, thereby providing strong support for further basic and application research in this bacterium.
期刊介绍:
Synthetic and Systems Biotechnology aims to promote the communication of original research in synthetic and systems biology, with strong emphasis on applications towards biotechnology. This journal is a quarterly peer-reviewed journal led by Editor-in-Chief Lixin Zhang. The journal publishes high-quality research; focusing on integrative approaches to enable the understanding and design of biological systems, and research to develop the application of systems and synthetic biology to natural systems. This journal will publish Articles, Short notes, Methods, Mini Reviews, Commentary and Conference reviews.