Article
Biotechnology & Applied Microbiology
Ke Liu, Gui-Hong Lin, Kun Liu, Yong-Jun Liu, Xin-Yi Tao, Bei Gao, Ming Zhao, Dong-Zhi Wei, Feng-Qing Wang
Summary: In this study, a multiplexed integrase-assisted site-specific recombination (miSSR) method was developed to integrate genes/pathways in Mycolicibacteria for the purpose of constructing cell factories. The method successfully integrated multiple copies of genes using different bacteriophage systems and a reconstructed Xer recombinase system. The results showed that the miSSR system is an effective and convenient tool for engineering the genomes of Mycolicibacteria and other related strains.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2022)
Article
Microbiology
Lauren A. Riley, Irenee C. Payne, Melissa Tumen-Velasquez, Adam M. Guss
Summary: This study developed a system for integrating up to 12 genetic constructs into the E. coli chromosome. Site-specific recombinases were used to catalyze recombination between specific DNA sequences, enabling the integration of heterologous DNA. The utility of this system was demonstrated by the insertion of eight DNA methyltransferases into the E. coli chromosome.
JOURNAL OF BACTERIOLOGY
(2023)
Article
Multidisciplinary Sciences
Joshua R. Elmore, Gara N. Dexter, Henri Baldino, Jay D. Huenemann, Ryan Francis, V. George L. Peabody, Jessica Martinez-Baird, Lauren A. Riley, Tuesday Simmons, Devin Coleman-Derr, Adam M. Guss, Robert G. Egbert
Summary: SAGE is a highly efficient and extensible genome engineering technology that allows selection marker-free, site-specific genome integration of multiple DNA constructs in bacteria. It shows superior efficiency compared to replicating plasmids and overcomes host range limitations. SAGE has the potential to expand high-throughput genetics and synthetic biology in industrial and environmental bacteria.
Article
Microbiology
Jing Yang, Lina Liu, Yu Feng, Da He, Chengcheng Wang, Zhiyong Zong
Summary: The newly identified mcr-10 plasmid-borne colistin resistance gene was found in a Cronobacter sakazakii isolate. It may be mobilized through site-specific recombination mediated by an integrase of an integrative mobile element.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Microbiology
Gang Zhang, Qinna Cui, Jianjuan Li, Ruiliang Guo, Sebastien Olivier Leclercq, Lifeng Du, Na Tang, Yuqin Song, Chao Wang, Fangqing Zhao, Jie Feng
Summary: In this study, the mobility of GIsul2 and CR2-sul2 units mediated by integrase was experimentally characterized. The results demonstrate that the integrase of GIsul2 can perform the excision and integration of GIsul2 and CR2-sul2 unit by site-specific recombination between att core sites. The findings suggest a potential and unappreciated role of the GIsul2 integrase family in the dissemination of CR2-sul2 units carrying various resistance determinants.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Vishnu Hosur, Benjamin E. Low, Michael V. Wiles
Summary: The inability to efficiently and precisely insert large DNA constructs into the genome is a major challenge in genomic engineering. Existing methods lack precision or have limited capacity. However, a new toolkit combining RNA-guided Cas9 and site-specific integrase Bxb1 has been developed, enabling the integration of DNA constructs ranging from 5 to 43 kb in mouse zygotes and human cells.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Adriana Adolfi, Amy Lynd, Gareth J. Lycett, Anthony A. James
Summary: The phi C31 system is a crucial genetic tool for the transgenic manipulation of malaria mosquitoes and other insect vectors, enabling precise modification of the Anopheles genome to achieve genetic control of malaria.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Microbiology
Helena Leinweber, Raphael N. Sieber, Jesper Larsen, Marc Stegger, Hanne Ingmer
Summary: The study revealed that phages carrying virulence factors can adapt and integrate into new strains of Staphylococcus aureus, even those lacking preferred integration sites. This adaptation is facilitated by the promiscuity of the phage-encoded tyrosine recombinase, allowing the phages to increase virulence and zoonotic potential in different host organisms.
Article
Biochemistry & Molecular Biology
Kimihiro Abe, Takumi Takahashi, Tsutomu Sato
Summary: This study demonstrates the importance of the extreme C-terminal region (ECT) of SprA in DNA recombination and directionality control in Bacillus subtilis. The interaction between SprA and SprB is influenced by the alanine residue Phe532 in the extreme C-terminal region, affecting the directional control of the recombination reaction.
MOLECULAR MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Gang Zhang, Shigang Yao, Yunan Liu, Hailing Fang, Yuqin Song, Chao Wang, Dawei Wei, Jie Feng
Summary: In this study, we identified 530 novel tyrosine-type integrases from bacterial genomic islands. These integrases belong to a distinct evolutionary clade and are affiliated with new integrase groups. The integration functions of six representative novel integrases were validated in a bacterial model system, and their expression patterns were confirmed in Escherichia coli. This study revealed site-specific recombination functions of novel integrases and expands the toolbox for genetic engineering.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Nafiseh Sanei Ata-Abadi, Mahboobeh Forouzanfar, Kianoush Dormiani, Shiva Rouhollahi Varnosfaderani, Leila Pirjamali, Mohammad Hossein Nasr-Esfahani, Reza Moradi Hajidavaloo
Summary: In this study, we successfully constructed stable cell lines in HEK293T cells using the PhiC31 integrase system, which can efficiently produce and secrete active rhPH20. Quantitative and functional analysis showed that the secreted rhPH20 had specific activity and could remove cumulus cells from oocytes. Additionally, the results demonstrated the ability of the PhiC31 enzyme to insert the PH20-expressing donors into specific pseudo attP sites in the genome of target cells with different copy numbers.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Veterinary Sciences
Ying Wang, Jianfeng Deng, Jianle Ren, Libin Liang, Junping Li, Sheng Niu, Xingchen Wu, Yujun Zhao, Shimin Gao, Fang Yan, Yuqing Liu, Haili Ma, Wen-xia Tian, Yi Yan
Summary: This study discovered two integrated genomic islands in Riemerella anatipestifer and investigated their relationship with the RAP44 phage genome. It was found that the phage genome was integrated into the R. anatipestifer chromosome, and comparative analysis revealed an evolutionary relationship between them. Additionally, the integrated defective phage sequence exhibited the functions of integration, excision, and cyclization automatically.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Microbiology
Sridhar Mandali, Reid C. Johnson
Summary: Bacteriophage serine integrases catalyze specific recombination reactions between DNA segments called att sites, with the help of a directionality factor. The integrases include a DNA-binding region with a recombinase domain and a zinc-binding domain, with unique coiled-coil motifs. Mutations in specific residues control the formation of synaptic complexes, with CC motifs playing a crucial role in recombination even after initial assembly. The site-specific recombination reactions promoted by these integrases are essential for the life cycle of bacteriophages and have potential applications in genetic engineering and synthetic biology.
JOURNAL OF BACTERIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Garima Jain, Helga Ertesvag
Summary: In this study, the homologous recombination method in Rhodococcus opacus was improved by constructing and evaluating a conjugative, conditional suicide plasmid based on a replicon derived from Corynebacterium glutamicum. The low recombination frequency issue was successfully solved. It was also discovered that mycolic acid is essential for the viability of R. opacus.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Review
Microbiology
Cheng Chang, Xinbo Yu, Wennan Guo, Chaoyi Guo, Xiaokui Guo, Qingtian Li, Yongzhang Zhu
Summary: Biofilms are complex microbial microcolonies that are resistant to antibiotics and can adhere to various surfaces. Using bacteriophages and their components for biofilm removal shows promise, but there are still challenges to overcome.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Lin Zhang, Eckhard Bill, Peter M. H. Kroneck, Oliver Einsle
Summary: Copper-containing nitrous oxide reductase (N2OR) is the only known enzyme capable of converting nitrous oxide to dinitrogen, with unique Cu-Z and CUA sites. Systematic mutagenesis of histidine and surrounding H-bonding residues revealed that only variants with protonable side chains like His, Asp, and Glu can mediate electron transfer at physiological pH.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemical Research Methods
Yujiao Yang, Hong Zhang, Zhenyang Guo, Siwei Zou, Fei Long, Jiacheng Wu, Peng Li, Guo-ping Zhao, Wei Zhao
Summary: The study identified abundant and dynamic acetylation in Streptomyces coelicolor, suggesting a possible competitive relationship with succinylation in regulating cell physiology. Knockout experiments and in vitro assays confirmed the regulatory crosstalk between the two sirtuins, laying a foundation for further characterization of lysine acetylation and succinylation interactions.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Biochemistry & Molecular Biology
Yongbiao Xue, Yiming Bao, Zhang Zhang, Wenming Zhao, Jingfa Xiao, Shun-min He, Guoqing Zhang, Yixue Li, Zhao Guoping, Runsheng Chen, Jingyao Zeng, Yadong Zhang, Yun-fei Shang, Jialin Mai, Shuo Shi, Mingming Lu, Congfan Bu, Zhewen Zhang, Zhenglin Du, Yinying Wang, Hongen Kang, Tianyi Xu, Lili Hao, Peilin Jia, Shuai Jiang, Qiheng Qian, Tong-tong Zhu, Yunfei Shang, Wenting Zong, Tong Jin, Yuansheng Zhang, Dong Zou, Zhang Zhang, Qiang Du, Changrui Feng, Lina Ma, Sisi Zhang, Anke Wang, Lili Dong, Yan-qing Wang, Wan Liu, Xing Yan, Yunchao Ling, Guoping Zhao, Zhihua Zhou, Wang Kang, Tao Zhang, Shuai Ma, Haoteng Yan, Zunpeng Liu, Zejun Ji, Yusheng Cai, Si Wang, Moshi Song, Jie Ren, Qi Zhou, Jing Qu, Weiqi Zhang, Guanghui Liu, Xu Chen, Tingting Chen, Zhang Sisi, Yanling Sun, Caixia Yu, Bixia Tang, Junwei Zhu, Shuang Zhai, Yubin Sun, Qiancheng Chen, Xiaoyu Yang, Xin Zhang, Zhengqi Sang, Yonggang Wang, Yilin Zhao, Huanxin Chen, Li Lan, Yanqing Wang, Yingke Ma, Yaokai Jia, Xin-chang Zheng, Meili Chen, Zou Dong, Tongtong Zhu, Chen Ming, Guangyi Niu, Rong Pan, Wei Jing, Jian Sang, Chang Liu, Yujia Xiong, Hao Lili, Mochen Zhang, Guoliang Wang, Lizhi Yi, Zhao Wei, Wenting Zong, Song Wu, Zhuang Xiong, Li Rujiao, Gong Zheng, Rujiao Li, Lin Liu, Zhao Li, Qianpeng Li, Jing Wei, Sicheng Luo, Jiajia Wang, Yirong Shi, Honghong Zhou, Peng Zhang, Tingrui Song, Yanyan Li, Fei Yang, Mengwei Li, Zhao-hua Li, Hongen Kang, Xinchang Zheng, Ru-jiao Li, Dongmei Tian, Xiaonan Liu, Cuiping Li, Xufei Teng, Shuhui Song, Yang Zhang, Guangyi Niu, Tongtong Zhu, Yuansheng Zhang, Ruru Chen, Rongqin Zhang, Feng Xu, Yifan Wang, Yunchao Ling, Chenfen Zhou, Haizhou Wang, Andrew E. Teschendorff, Yungang He, Yang Zhen, Cuiping Li, Junwei Zhu, Lun Li, Na Li, Zheng Gong, Meili Chen, Ying Cui, Guangya Duan, Jin Tong, Gangao Wu, Tianhao Huang, Enhui Jin, Wei Zhao, Hailong Kang, Zhonghuang Wang, Jingyao Zeng, Hua Chen, Mingkun Li, Wenming Zhao, Wanshan Ning, Yu Xue, Yanhu Liu, Ying Cui, Qijun Zhou, Xingyan Liu, Longlong Zhang, Bingyu Mao, Shihua Zhang, Yaping Zhang, Guodong Wang, Qianghui Zhu, Xin Li, Menghua Li, Yuanming Liu, Hong Luo, Xiaoyuan Wu, Haichun Jing, Yitong Pan, Ming Chen, Lina Ma, Leisheng Shi, Mingkun Li, Li Lan, Yiming Bao, Wen-ming Zhao, Zhixiang Zuo, Jian Ren, Xinxin Zhang, Yun Xiao, Xia Li, Dan Liu, Chi Zhang, Yu Xue, Zheng Zhao, Tao Jiang, Wanying Wu, Fangqing Zhao, Xianwen Meng, Di Peng, Hao Luo, Feng Gao, Shaofeng Lin, Chuijie Liu, Anyuan Guo, Hao Yuan, Tianhan Su, Yong E. Zhang, Yincong Zhou, Weizhi Zhang, Shanshan Fu, Xiaodan Tan, Yubin Xie, Guoji Guo, Chenwei Wang, Xingyu Liao, Xin Gao, Jianxin Wang, Guiyan Xie, Chunhui Yuan, Feng Tian, Dechang Yang, Dachao Tang, Wenyi Wu, Yujie Gou, Cheng Han, Qinghua Cui, Xiang Shang Li, Chuan-Yun Li, XiaoTong Luo, Jia Ren, Xia Li
Summary: The National Genomics Data Center (NGDC) of China National Center for Bioinformation (CNCB) provides database resources to support global research, with a focus on single-cell omics and precision medicine. They continuously scale up and update core database resources, daily update SARS-CoV-2 genome data, and establish OpenLB and update Database Commons.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Immunology
Mengying Wu, Wenyan Shan, Guo-Ping Zhao, Liang-Dong Lyu
Summary: This study reveals the gene expression kinetics of Mycobacterium tuberculosis under different intensities of oxidative stress, providing unique insights into their antioxidant defense strategies.
EMERGING MICROBES & INFECTIONS
(2022)
Editorial Material
Multidisciplinary Sciences
Yunchao Ling, Ruifang Cao, Jiaqiang Qian, Jiefu Li, Haokui Zhou, Liyun Yuan, Zhen Wang, Liangxiao Ma, Guangyong Zheng, Guoping Zhao, Zefeng Wang, Guoqing Zhang, Yixue Li
Article
Multidisciplinary Sciences
Yuchen Wang, Yuting Tang, Chen Lin, Junli Zhang, Juntao Mai, Jun Jiang, Xiaoxiao Gao, Yao Li, Guoping Zhao, Lu Zhang, Jun Liu
Summary: The ESX-4 system in Mycobacterium marinum does not secrete its cognate substrates, but the deletion of eccC4, an essential component of ESX-4, resulted in elevated secretion of protein substrates of ESX-1 and ESX-5, leading to enhanced phagocytosis by macrophages.
Article
Microbiology
Hong Zou, Man Zhang, Xiaoting Zhu, Liyan Zhu, Shuo Chen, Mingjing Luo, Qinglian Xie, Yue Chen, Kangxi Zhang, Qingyun Bu, Yuchen Wei, Tao Ye, Qiang Li, Xing Yan, Zhihua Zhou, Chen Yang, Yu Li, Haokui Zhou, Chenhong Zhang, Xiaoyan You, Guangyong Zheng, Guoping Zhao
Summary: Ginsenoside Rb1 improves metabolic disorders in high-fat diet mice by modulating the gut microbiota and intestinal free fatty acids profiles.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Pharmacology & Pharmacy
Lingli Ding, Song Gu, Bingyu Zhou, Min Wang, Yage Zhang, Siluo Wu, Hong Zou, Guoping Zhao, Zhao Gao, Liangliang Xu
Summary: Fractures have a negative impact on an individual's quality of life, but Ginsenoside Compound K (CK) found in Ginseng has shown potential for promoting bone regeneration and angiogenesis. This study found that CK can promote osteogenic differentiation of rat bone marrow mesenchymal stem cells and increase tube formation capacity in human umbilical vein endothelial cells. In a rat open femoral fracture model, CK was found to improve fracture repair and increase the formation of H type vessel in the fracture callus.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Multidisciplinary Sciences
Christoph Mueller, Lin Zhang, Sara Zipfel, Annika Topitsch, Marleen Lutz, Johannes Eckert, Benedikt Prasser, Mohamed Chami, Wei Lu, Juan Du, Oliver Einsle
Summary: This study presents a mechanism of copper trafficking and assembly mediated by NosDFY, NosL, and N2OR, which is facilitated by ATP hydrolysis. This mechanism provides new structural insights to understand critical climate change and environmental issues.
Article
Immunology
Hongguan Xing, Liyan Zhu, Pingping Wang, Guoping Zhao, Zhihua Zhou, Yi Yang, Hong Zou, Xing Yan
Summary: Yeas surface display technology can provide a low-cost alternative for rapid large-scale preparation of promising SARS-CoV-2 vaccine candidates. Vaccination with B.1.617.1 variant induces robust immune responses and possesses neutralizing antibody activity against wild-type and variant strains.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Microbiology
Jiangang Ma, Wei Zhou, Jing Wu, Xiaofeng Liu, Jiahui Lin, Xiaofeng Ji, Hui Lin, Jianmei Wang, Han Jiang, Qianjin Zhou, Guoping Zhao, Hua Yang, Biao Tang
Summary: Widely distributed multidrug-resistant bacteria pose a threat to animal and human health, but there have been few surveys on the antimicrobial resistance of large-scale animal-derived bacteria. A study in Zhejiang Province, China, found that Escherichia coli strains isolated from pig and chicken anal swab samples showed high resistance to multiple antibiotics, and some strains carried resistance genes against last-resort antimicrobials. Furthermore, a correlation between heavy metals and antibiotic resistance was observed.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biology
Bowen Zhan, Yanqing Gao, Wenqing Gao, Ye Li, Zhengyang Li, Qi Qi, Xin Lan, Hongbo Shen, Jianhua Gan, Guoping Zhao, Jixi Li
Summary: Crystal structures of M. tuberculosis elongation factors EF-Tu and EF-Ts in complex and GDP-bound Ef-Tu reveal the molecular basis of EF-Tu's representative recycling and inactive forms in protein translation. The FDA-approved drug Osimertinib inhibits the growth of related strains by directly binding with EF-Tu.
COMMUNICATIONS BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Pawel Lycus, Oliver Einsle, Lin Zhang
Summary: Microbial metabolic processes drive the global nitrogen cycle through metalloenzymes that facilitate redox reactions at ambient conditions. Recent developments in spectroscopy and structural biology have provided powerful tools for understanding nitrogen metabolism and its environmental implications. This review focuses on the contributions of structural biology to nitrogen metabolism and highlights the potential for biotechnological applications to manage the global nitrogen cycle.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2023)
Article
Microbiology
Biao Tang, Jiang Chang, Yifei Chen, Jiahui Lin, Xingning Xiao, Xiaodong Xia, Jun Lin, Hua Yang, Guoping Zhao
Summary: The prevalence and antimicrobial resistance of E. fergusonii in food animals in China were investigated, revealing a high diversity in prevalence and high levels of antimicrobial resistance. E. fergusonii may serve as an important reservoir of antimicrobial resistance genes, particularly mcr-1.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biology
Wei Tan, Zhi-Hui Shao, Guo-Ping Zhao
Summary: Nitrate serves as a major inorganic nitrogen source for microorganisms, with many bacterial and archaeal lineages expressing cytoplasmic assimilatory nitrate reductase (NAS) to catalyze the reduction of nitrate to nitrite. This study presents a detailed protocol for measuring in vitro nitrate reductase (NaR) activity of NAS enzymes from Mycolicibacterium smegmatis crude extract using both physiological and non-physiological electron donors.