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Wang ZJ, Liu X, Zhou H, Liu Y, Zhong L, Wang X, Tu Q, Huo L, Yan F, Gu L, Müller R, Zhang Y, Bian X, Xu X. Engineering of Burkholderia thailandensis strain E264 serves as a chassis for expression of complex specialized metabolites. Front Microbiol 2022; 13:1073243. [PMID: 36466684 PMCID: PMC9712229 DOI: 10.3389/fmicb.2022.1073243] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/28/2022] [Indexed: 09/16/2023] Open
Abstract
Heterologous expression is an indispensable approach to exploiting natural products from phylogenetically diverse microbial communities. In this study, we constructed a heterologous expression system based on strain Burkholderia thailandensis E264 by deleting efflux pump genes and screening constitutive strong promoters. The biosynthetic gene cluster (BGC) of disorazol from Sorangium cellulosum So ce12 was expressed successfully with this host, and the yield of its product, disorazol F2, rather than A1, was improved to 38.3 mg/L by promoter substitution and insertion. In addition to the disorazol gene cluster, the BGC of rhizoxin from Burkholderia rhizoxinica was also expressed efficiently, whereas no specific peak was detected when shuangdaolide BGC from Streptomyces sp. B59 was transformed into the host. This system provides another option to explore natural products from different phylogenetic taxa.
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Affiliation(s)
- Zong-Jie Wang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiaotong Liu
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yang Liu
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lin Zhong
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xue Wang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qiang Tu
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liujie Huo
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Fu Yan
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lichuan Gu
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarbrücken, Germany
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiaokun Xu
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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2
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Genome-based taxonomic classification of the closest-to-Comamonadaceae group supports a new family Sphaerotilaceae fam. nov. and taxonomic revisions. Syst Appl Microbiol 2022; 45:126352. [DOI: 10.1016/j.syapm.2022.126352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/06/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022]
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3
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Chen H, Zhong L, Zhou H, Sun T, Zhong G, Tu Q, Zhuang Y, Bai X, Wang X, Xu J, Xia L, Shen Y, Zhang Y, Bian X. Biosynthesis of Glidomides and Elucidation of Different Mechanisms for Formation of β-OH Amino Acid Building Blocks. Angew Chem Int Ed Engl 2022; 61:e202203591. [PMID: 35689369 DOI: 10.1002/anie.202203591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 11/06/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) can incorporate nonproteinogenic amino acids into peptidyl backbones to increase structural diversity. Genome mining of Schlegelella brevitalea led to the identification of a class of linear lipoheptapeptides, glidomides, featuring two unusual residues: threo-β-OH-L-His and threo-β-OH-D-Asp. The β-hydroxylation of Asp and His is catalyzed by the nonheme FeII /α-ketoglutarate-dependent β-hydroxylases GlmD and GlmF, respectively. GlmD independently catalyzes the hydroxylation of L-Asp to primarily produce threo-β-OH-L-Asp on the thiolation domain, and then undergoes epimerization to form threo-β-OH-D-Asp in the final products. However, β-hydroxylation of His requires the concerted action of GlmF and the interface (I) domain, a novel condensation domain family clade. The key sites of I domain for interaction with GlmF were identified, suggesting that the mechanism for hydroxylation of His depends on the collaboration between hydroxylase and NRPS.
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Affiliation(s)
- Hanna Chen
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Lin Zhong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Tao Sun
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Guannan Zhong
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Qiang Tu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yan Zhuang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xianping Bai
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xingyan Wang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Jiaying Xu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yuemao Shen
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
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4
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Chen H, Zhong L, Zhou H, Sun T, Zhong G, Tu Q, Zhuang Y, Bai X, Wang X, Xu J, Xia L, Shen Y, Zhang Y, Bian X. Biosynthesis of Glidomides and Elucidation of Different Mechanisms for Formation of β‐OH Amino Acid Building Blocks. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hanna Chen
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Lin Zhong
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- Faculty of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Tao Sun
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Guannan Zhong
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Qiang Tu
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- Faculty of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Yan Zhuang
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Xianping Bai
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Xingyan Wang
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Jiaying Xu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology State Key Laboratory of Developmental Biology of Freshwater Fish College of Life Science Hunan Normal University Changsha 410081 China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology State Key Laboratory of Developmental Biology of Freshwater Fish College of Life Science Hunan Normal University Changsha 410081 China
| | - Yuemao Shen
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- Faculty of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
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Liu J, Wang X, Dai G, Zhang Y, Bian X. Microbial chassis engineering drives heterologous production of complex secondary metabolites. Biotechnol Adv 2022; 59:107966. [PMID: 35487394 DOI: 10.1016/j.biotechadv.2022.107966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
Abstract
The cryptic secondary metabolite biosynthetic gene clusters (BGCs) far outnumber currently known secondary metabolites. Heterologous production of secondary metabolite BGCs in suitable chassis facilitates yield improvement and discovery of new-to-nature compounds. The two juxtaposed conventional model microorganisms, Escherichia coli, Saccharomyces cerevisiae, have been harnessed as microbial chassis to produce a bounty of secondary metabolites with the help of certain host engineering. In last decade, engineering non-model microbes to efficiently biosynthesize secondary metabolites has received increasing attention due to their peculiar advantages in metabolic networks and/or biosynthesis. The state-of-the-art synthetic biology tools lead the way in operating genetic manipulation in non-model microorganisms for phenotypic optimization or yields improvement of desired secondary metabolites. In this review, we firstly discuss the pros and cons of several model and non-model microbial chassis, as well as the importance of developing broader non-model microorganisms as alternative programmable heterologous hosts to satisfy the desperate needs of biosynthesis study and industrial production. Then we highlight the lately advances in the synthetic biology tools and engineering strategies for optimization of non-model microbial chassis, in particular, the successful applications for efficient heterologous production of multifarious complex secondary metabolites, e.g., polyketides, nonribosomal peptides, as well as ribosomally synthesized and post-translationally modified peptides. Lastly, emphasis is on the perspectives of chassis cells development to access the ideal cell factory in the artificial intelligence-driven genome era.
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Affiliation(s)
- Jiaqi Liu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China; Present address: Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Guangzhi Dai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China.
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6
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Wang X, Zheng W, Zhou H, Tu Q, Tang YJ, Stewart AF, Zhang Y, Bian X. Improved dsDNA recombineering enables versatile multiplex genome engineering of kilobase-scale sequences in diverse bacteria. Nucleic Acids Res 2021; 50:e15. [PMID: 34792175 PMCID: PMC8860599 DOI: 10.1093/nar/gkab1076] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 09/23/2021] [Accepted: 10/22/2021] [Indexed: 01/21/2023] Open
Abstract
Recombineering assisted multiplex genome editing generally uses single-stranded oligonucleotides for site directed mutational changes. It has proven highly efficient for functional screens and to optimize microbial cell factories. However, this approach is limited to relatively small mutational changes. Here, we addressed the challenges involved in the use of double-stranded DNA substrates for multiplex genome engineering. Recombineering is mediated by phage single-strand annealing proteins annealing ssDNAs into the replication fork. We apply this insight to facilitate the generation of ssDNA from the dsDNA substrate and to alter the speed of replication by elevating the available deoxynucleoside triphosphate (dNTP) levels. Intracellular dNTP concentration was elevated by ribonucleotide reductase overexpression or dNTP addition to establish double-stranded DNA Recombineering-assisted Multiplex Genome Engineering (dReaMGE), which enables rapid and flexible insertional and deletional mutagenesis at multiple sites on kilobase scales in diverse bacteria without the generation of double-strand breaks or disturbance of the mismatch repair system. dReaMGE can achieve combinatorial genome engineering works, for example, alterations to multiple biosynthetic pathways, multiple promoter or gene insertions, variations of transcriptional regulator combinations, within a few days. dReaMGE adds to the repertoire of bacterial genome engineering to facilitate discovery, functional genomics, strain optimization and directed evolution of microbial cell factories.
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Affiliation(s)
- Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Wentao Zheng
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Qiang Tu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Ya-Jie Tang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
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Wang J, Ran Q, Du X, Wu S, Wang J, Sheng D, Chen Q, Du Z, Li YZ. Two new Polyangium species, P. aurulentum sp. nov. and P. jinanense sp. nov., isolated from a soil sample. Syst Appl Microbiol 2021; 44:126274. [PMID: 34763291 DOI: 10.1016/j.syapm.2021.126274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 11/18/2022]
Abstract
Polyangium belongs to Polyangiaceae family of Myxococcales, a taxonomic group well-known for their extraordinary social lifestyle and diverse novel gene clusters of secondary metabolites. A yellow-golden strain, designated SDU3-1T, and two rose pink strains, designated SDU13 and SDU14T, were isolated from a soil sample. These three strains were aerobic, mesophilic, not salt-tolerant and were able to prey on living microorganisms. SDU13 and SDU14T formed solitary sporangioles under starvation conditions, while SDU3-1T had no fruiting body structures. They showed 95.9-97.0% (SDU3-1T) or 98.7-98.9% (SDU13 and SDU14T) 16S rRNA gene similarity with the type strains of Polyangium, but were phylogenetically separate from them based on the 16S rRNA gene and genome sequences. Their genomes were 12.3 Mbp (SDU3-1T), 13.9 Mbp (SDU13) and 13.8 Mbp (SDU14T) with the G + C content range of 68.3-69.4 mol%. The average nucleotide identity and DNA-DNA hybridization analyses of genomes further indicated that these three strains belonged to two new species in Polyangium. Their major fatty acids were C18:1ω9c, C16:0 and C18:0. The polyphasic taxonomic characterization suggest that the three strains represent two novel species in the genus Polyangium, for which the names Polyangium aurulentum sp. nov. and Polyangium jinanense sp. nov. are proposed, and the type strains are SDU3-1T (=CGMCC 1.16875T = KCTC 72136T) and SDU14T (=CCTCC AB 2021123T = KCTC 82625T), respectively.
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Affiliation(s)
- Jingjing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Qi Ran
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Xinran Du
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Shuge Wu
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Jianing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Duohong Sheng
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Qi Chen
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Zongjun Du
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China; College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China.
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From Cell-Free Protein Synthesis to Whole-Cell Biotransformation: Screening and Identification of Novel α-Ketoglutarate-Dependent Dioxygenases for Preparative-Scale Synthesis of Hydroxy-l-Lysine. Catalysts 2021. [DOI: 10.3390/catal11091038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The selective hydroxylation of non-activated C-H bonds is still a challenging reaction in chemistry. Non-heme Fe2+/α-ketoglutarate-dependent dioxygenases are remarkable biocatalysts for the activation of C-H-bonds, catalyzing mainly hydroxylations. The discovery of new Fe2+/α-ketoglutarate-dependent dioxygenases with suitable reactivity for biotechnological applications is therefore highly relevant to expand the limited range of enzymes described so far. In this study, we performed a protein BLAST to identify homologous enzymes to already described lysine dioxygenases (KDOs). Six novel and yet uncharacterized proteins were selected and synthesized by cell-free protein synthesis (CFPS). The subsequent in vitro screening of the selected homologs revealed activity towards the hydroxylation of l-lysine (Lys) into hydroxy-l-lysine (Hyl), which is a versatile chiral building block. With respect to biotechnological application, Escherichia coli whole-cell biocatalysts were developed and characterized in small-scale biotransformations. As the whole-cell biocatalyst expressing the gene coding for the KDO from Photorhabdus luminescens showed the highest specific activity of 8.6 ± 0.6 U gCDW−1, it was selected for the preparative synthesis of Hyl. Multi-gram scale product concentrations were achieved providing a good starting point for further bioprocess development for Hyl production. A systematic approach was established to screen and identify novel Fe2+/α-ketoglutarate-dependent dioxygenases, covering the entire pathway from gene to product, which contributes to accelerating the development of bioprocesses for the production of value-added chemicals.
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Yolken R, Prandovszky E, Severance EG, Hatfield G, Dickerson F. The oropharyngeal microbiome is altered in individuals with schizophrenia and mania. Schizophr Res 2021; 234:51-57. [PMID: 32334937 DOI: 10.1016/j.schres.2020.03.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/02/2020] [Accepted: 03/05/2020] [Indexed: 01/10/2023]
Abstract
It is being increasingly recognized that human mucosal surfaces are not sterile but are colonized with microorganisms collectively known as the microbiome. The microbiome can alter brain functioning in humans and animals by way of a series of interactions operative in the brain-immune-gut interactome. We characterized the oropharyngeal microbiome in 316 individuals, including 121 with schizophrenia, 62 with mania, 48 with major depressive disorder, and 85 controls without a psychiatric disorder. We found that the oropharyngeal microflora of individuals with schizophrenia and individuals with mania differed from controls in composition and abundance as measured by the weighted UniFrac distance (both p < .003 adjusted for covariates and multiple comparisons). This measure in individuals with major depressive disorder did not differ from that of controls. We also identified five bacterial taxa which differed among the diagnostic groups. Three of the taxa, Neisseria subflava, Weeksellaceae, and Prevotella, were decreased in individuals with schizophrenia or mania as compared to controls, while Streptococci was increased in these groups. One taxa, Schlegelella, was only found in individuals with mania. Neisseria subflava was also positively associated with cognitive functioning as measured by the Repeatable Battery for the Assessment of Neuropsychological Status. There were no taxa significantly altered in individuals with major depression. Individuals with schizophrenia and mania have altered compositions of the oropharyngeal microbiome. An understanding of the biology of the microbiome and its effect on the brain might lead to new insights into the pathogenesis, and ultimately, the prevention and treatment of these disorders.
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Affiliation(s)
- Robert Yolken
- Stanley Neurovirology Laboratory, Johns Hopkins School of Medicine, United States of America.
| | - Emese Prandovszky
- Stanley Neurovirology Laboratory, Johns Hopkins School of Medicine, United States of America
| | - Emily G Severance
- Stanley Neurovirology Laboratory, Johns Hopkins School of Medicine, United States of America
| | - Glen Hatfield
- Stanley Neurovirology Laboratory, Johns Hopkins School of Medicine, United States of America
| | - Faith Dickerson
- Stanley Neurovirology Laboratory, Johns Hopkins School of Medicine, United States of America
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Li R, Shi H, Zhao X, Liu X, Duan Q, Song C, Chen H, Zheng W, Shen Q, Wang M, Wang X, Gong K, Yin J, Zhang Y, Li A, Fu J. Development and application of an efficient recombineering system for Burkholderia glumae and Burkholderia plantarii. Microb Biotechnol 2021; 14:1809-1826. [PMID: 34191386 PMCID: PMC8313284 DOI: 10.1111/1751-7915.13840] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 02/07/2023] Open
Abstract
The lambda phage Red proteins Redα/Redβ/Redγ and Rac prophage RecE/RecT proteins are powerful tools for precise and efficient genetic manipulation but have been limited to only a few prokaryotes. Here, we report the development and application of a new recombineering system for Burkholderia glumae and Burkholderia plantarii based on three Rac bacteriophage RecET-like operons, RecETheBDU8 , RecEThTJI49 and RecETh1h2eYI23 , which were obtained from three different Burkholderia species. Recombineering experiments indicated that RecEThTJI49 and RecETh1h2eYI23 showed higher recombination efficiency compared to RecETheBDU8 in Burkholderia glumae PG1. Furthermore, all of the proteins currently categorized as hypothetical proteins in RecETh1h2eYI23, RecEThTJI49 and RecETheBDU8 may have a positive effect on recombination in B. glumae PG1 except for the h2 protein in RecETh1h2eYI23 . Additionally, RecETYI23 combined with exonuclease inhibitors Pluγ or Redγ exhibited equivalent recombination efficiency compared to Redγβα in Escherichia coli, providing potential opportunity of recombineering in other Gram-negative bacteria for its loose host specificity. Using recombinase-assisted in situ insertion of promoters, we successfully activated three cryptic non-ribosomal peptide synthetase biosynthetic gene clusters in Burkholderia strains, resulting in the generation of a series of lipopeptides that were further purified and characterized. Compound 7 exhibited significant potential anti-inflammatory activity by inhibiting lipopolysaccharide-stimulated nitric oxide production in RAW 264.7 macrophages. This recombineering system may greatly enhance functional genome research and the mining of novel natural products in the other species of the genus Burkholderia after optimization of a protocol.
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Affiliation(s)
- Ruijuan Li
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Hongbo Shi
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Xiaoyu Zhao
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Xianqi Liu
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Qiong Duan
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Chaoyi Song
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Hanna Chen
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Wentao Zheng
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Qiyao Shen
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Maoqin Wang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Xue Wang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Kai Gong
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Jia Yin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationCollege of Life SciencesHunan Normal UniversityChangshaHunan410081China
| | - Youming Zhang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Aiying Li
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
| | - Jun Fu
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoShandong266237People’s Republic of China
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Shrivastava A, Sharma RK. Myxobacteria and their products: current trends and future perspectives in industrial applications. Folia Microbiol (Praha) 2021; 66:483-507. [PMID: 34060028 DOI: 10.1007/s12223-021-00875-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 05/13/2021] [Indexed: 12/12/2022]
Abstract
Myxobacteria belong to a group of bacteria that are known for their well-developed communication system and synchronized or coordinated movement. This typical behavior of myxobacteria is mediated through secondary metabolites. They are capable of producing secondary metabolites belonging to several chemical classes with unique and wide spectrum of bioactivities. It is predominantly significant that myxobacteria specialize in mechanisms of action that are very rare with other producers. Most of the metabolites have been explored for their medical and pharmaceutical values while a lot of them are still unexplored. This review is an attempt to understand the role of potential metabolites produced by myxobacteria in different applications. Different myxobacterial metabolites have demonstrated antibacterial, antifungal, and antiviral properties along with cytotoxic activity against various cell lines. Beside their metabolites, these myxobacteria have also been discussed for better exploitation and implementation in different industrial sectors.
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Affiliation(s)
- Akansha Shrivastava
- Department of Biosciences, Manipal University Jaipur, Rajasthan, 303007, Jaipur, India
| | - Rakesh Kumar Sharma
- Department of Biosciences, Manipal University Jaipur, Rajasthan, 303007, Jaipur, India.
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12
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Zheng W, Wang X, Zhou H, Zhang Y, Li A, Bian X. Establishment of recombineering genome editing system in Paraburkholderia megapolitana empowers activation of silent biosynthetic gene clusters. Microb Biotechnol 2021; 13:397-405. [PMID: 32053291 PMCID: PMC7017819 DOI: 10.1111/1751-7915.13535] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/12/2019] [Accepted: 12/30/2019] [Indexed: 12/30/2022] Open
Abstract
The Burkholderiales are an emerging source of bioactive natural products. Their genomes contain a large number of cryptic biosynthetic gene clusters (BGCs), indicating great potential for novel structures. However, the lack of genetic tools for the most of Burkholderiales strains restricts the mining of these cryptic BGCs. We previously discovered novel phage recombinases Redαβ7029 from Burkholderiales strain DSM 7029 that could help in efficiently editing several Burkholderiales genomes and established the recombineering genome editing system in Burkholderialse species. Herein, we report the application of this phage recombinase system in another species Paraburkholderia megapolitana DSM 23488, resulting in activation of two silent non‐ribosomal peptide synthetase/polyketide synthase BGCs. A novel class of lipopeptide, haereomegapolitanin, was identified through spectroscopic characterization. Haereomegapolitanin A represents an unusual threonine‐tagged lipopeptide which is longer than the predicted NRPS assembly line. This recombineering‐mediated genome editing system shows great potential for genetic manipulation of more Burkholderiales species to activate silent BGCs for bioactive metabolites discovery.
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Affiliation(s)
- Wentao Zheng
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
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Schlegelella koreensis sp. nov., isolated from evaporator core of automobile air conditioning system. Arch Microbiol 2021; 203:2373-2378. [PMID: 33661313 DOI: 10.1007/s00203-021-02206-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/18/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
A white-coloured, aerobic, and rod-shaped bacterium, designated strain ID0723T was isolated from evaporator core of automobile air conditioning system. The strain was Gram-stain-negative, catalase positive, oxidase negative, and grew at pH 5.5-9.5, at temperature 18-37 °C, and at 0-2.0% (w/v) NaCl concentration. The phylogenetic analysis and 16S rRNA gene sequence data revealed that the strain ID0723T was affiliated to the genus Schlegelella, with the closest phylogenetic member being Schlegelella brevitalea DSM 7029 T (98.1% sequence similarity). The chemotaxonomic features of strain ID0723T were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine as the main polar lipids; Q-8 as an only ubiquinone; and summed feature 3 (C16:1ω7c and/or C16: 1ω6c), C16:0, and summed feature 8 (C18:1ω7c/or C18:1ω6c) as the major fatty acids. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization values between strain ID0723T and S. brevitalea DSM 7029 T were 74.8% and 20.0%, respectively, which were below the cut-off values of 95% and 70%, respectively. The DNA G + C content was 69.9 mol%. The polyphasic taxonomic data clearly indicated that strain ID0723T represents a novel species in the genus Schlegelella for which the name Schlegelella koreensis sp. nov. is proposed, with the type strain ID0723T (= KCTC 72731 T = NBRC 114611 T).
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Genomics-Driven Activation of Silent Biosynthetic Gene Clusters in Burkholderia gladioli by Screening Recombineering System. Molecules 2021; 26:molecules26030700. [PMID: 33572733 PMCID: PMC7866175 DOI: 10.3390/molecules26030700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 01/10/2023] Open
Abstract
The Burkholderia genus possesses ecological and metabolic diversities. A large number of silent biosynthetic gene clusters (BGCs) in the Burkholderia genome remain uncharacterized and represent a promising resource for new natural product discovery. However, exploitation of the metabolomic potential of Burkholderia is limited by the absence of efficient genetic manipulation tools. Here, we screened a bacteriophage recombinase system Redγ-BAS, which was functional for genome modification in the plant pathogen Burkholderia gladioli ATCC 10248. By using this recombineering tool, the constitutive promoters were precisely inserted in the genome, leading to activation of two silent nonribosomal peptide synthetase gene clusters (bgdd and hgdd) and production of corresponding new classes of lipopeptides, burriogladiodins A–H (1–8) and haereogladiodins A–B (9–10). Structure elucidation revealed an unnatural amino acid Z- dehydrobutyrine (Dhb) in 1–8 and an E-Dhb in 9–10. Notably, compounds 2–4 and 9 feature an unusual threonine tag that is longer than the predicted collinearity assembly lines. The structural diversity of burriogladiodins was derived from the relaxed substrate specificity of the fifth adenylation domain as well as chain termination conducted by water or threonine. The recombinase-mediating genome editing system is not only applicable in B. gladioli, but also possesses great potential for mining meaningful silent gene clusters from other Burkholderia species.
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Zhong L, Diao X, Zhang N, Li F, Zhou H, Chen H, Bai X, Ren X, Zhang Y, Wu D, Bian X. Engineering and elucidation of the lipoinitiation process in nonribosomal peptide biosynthesis. Nat Commun 2021; 12:296. [PMID: 33436600 PMCID: PMC7804268 DOI: 10.1038/s41467-020-20548-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/02/2020] [Indexed: 12/18/2022] Open
Abstract
Nonribosomal peptide synthetases containing starter condensation domains direct the biosynthesis of nonribosomal lipopeptides, which generally exhibit wide bioactivities. The acyl chain has strong impacts on bioactivity and toxicity, but the lack of an in-depth understanding of starter condensation domain-mediated lipoinitiation limits the bioengineering of NRPSs to obtain novel derivatives with desired acyl chains. Here, we show that the acyl chains of the lipopeptides rhizomide, holrhizin, and glidobactin were modified by engineering the starter condensation domain, suggesting a workable approach to change the acyl chain. Based on the structure of the mutated starter condensation domain of rhizomide biosynthetic enzyme RzmA in complex with octanoyl-CoA and related point mutation experiments, we identify a set of residues responsible for the selectivity of substrate acyl chains and extend the acyl chains from acetyl to palmitoyl. Furthermore, we illustrate three possible conformational states of starter condensation domains during the reaction cycle of the lipoinitiation process. Our studies provide further insights into the mechanism of lipoinitiation and the engineering of nonribosomal peptide synthetases.
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Affiliation(s)
- Lin Zhong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xiaotong Diao
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Na Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Fengwei Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Hanna Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xianping Bai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xintong Ren
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.
| | - Dalei Wu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.
- Suzhou Research Institute, Shandong University, Suzhou, Jiangsu, 215123, China.
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.
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Liang J, Wang H, Bian X, Zhang Y, Zhao G, Ding X. Heterologous redox partners supporting the efficient catalysis of epothilone B biosynthesis by EpoK in Schlegelella brevitalea. Microb Cell Fact 2020; 19:180. [PMID: 32933531 PMCID: PMC7493146 DOI: 10.1186/s12934-020-01439-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/10/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Epothilone B is a natural product that stabilizes microtubules, similar to paclitaxel (Taxol); therefore, epothilone B and several derivatives have shown obvious antitumour activities. Some of these products are in clinical trials, and one (ixabepilone, BMS) is already on the market, having been approved by the FDA in 2007. The terminal step in epothilone B biosynthesis is catalysed by the cytochrome P450 enzyme EpoK (CYP167A1), which catalyses the epoxidation of the C12-C13 double bond (in epothilone C and D) to form epothilone A and B, respectively. Although redox partners from different sources support the catalytic activity of EpoK in vitro, the conversion rates are low, and these redox partners are not applied to produce epothilone B in heterologous hosts. RESULTS Schlegelella brevitalea DSM 7029 contains electron transport partners that efficiently support the catalytic activity of EpoK. We screened and identified one ferredoxin, Fdx_0135, by overexpressing putative ferredoxin genes in vivo and identified two ferredoxin reductases, FdR_0130 and FdR_7100, by whole-cell biotransformation of epothilone C to effectively support the catalytic activity of EpoK. In addition, we obtained strain H7029-3, with a high epothilone B yield and found that the proportion of epothilone A + B produced by this strain was 90.93%. Moreover, the whole-cell bioconversion strain 7029-10 was obtained; this strain exhibited an epothilone C conversion rate of 100% in 12 h. Further RT-qPCR experiments were performed to analyse the overexpression levels of the target genes. Gene knock-out experiments showed that the selected ferredoxin (Fdx_0135) and its reductases (FdR_0130 and FdR_7100) might participate in critical physiological processes in DSM 7029. CONCLUSION Gene overexpression and whole-cell biotransformation were effective methods for identifying the electron transport partners of the P450 enzyme EpoK. In addition, we obtained an epothilone B high-yield strain and developed a robust whole-cell biotransformation system. This strain and system hold promise for the industrial production of epothilone B and its derivatives.
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Affiliation(s)
- Junheng Liang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Huimin Wang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Xiaoying Bian
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, Shandong, People's Republic of China
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, Shandong, People's Republic of China
| | - Guoping Zhao
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China.,CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Xiaoming Ding
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China.
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Yu Y, Wang H, Tang B, Liang J, Zhang L, Wang H, Bian X, Li YZ, Zhang Y, Zhao GP, Ding X. Reassembly of the Biosynthetic Gene Cluster Enables High Epothilone Yield in Engineered Schlegelella brevitalea. ACS Synth Biol 2020; 9:2009-2022. [PMID: 32603592 DOI: 10.1021/acssynbio.0c00100] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Epothilones, as a new class of microtubule-stabilizing anticancer drugs, exhibit strong bioactivity against taxane-resistant cells and show clinical activity for the treatment of advanced breast cancer. Additionally, they also show great potential for a central nervous system injury and Alzheimer's disease. However, due to the long fermentation period of the original producer and challenges of genetic engineering of nonribosomal peptide/polyketide (NRP/PK) megasynthase genes, the application of epothilones is severely limited. Here, we addressed these problems by reassembling a novel 56-kb epothilone biosynthetic gene cluster, optimizing the promoter of each gene based on RNA-seq profiling, and completing precursor synthetic pathways in engineered Schlegella brevitalea. Furthermore, we debottlenecked the cell autolysis by optimizing culture conditions. Finally, the yield of epothilones in shake flasks was improved to 82 mg/L in six-day fermentation. Overall, we not only constructed epothilone overproducers for further drug development but also provided a rational strategy for high-level NRP/PK compound production.
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Affiliation(s)
- Yucong Yu
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People’s Republic of China
| | - Huimin Wang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People’s Republic of China
| | - Biao Tang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People’s Republic of China
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, People’s Republic of China
| | - Junheng Liang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People’s Republic of China
| | - Lin Zhang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People’s Republic of China
| | - Hongkuan Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, People’s Republic of China
| | - Xiaoying Bian
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
| | - Yue-zhong Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
| | - Guo-ping Zhao
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People’s Republic of China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, People’s Republic of China
| | - Xiaoming Ding
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200438, People’s Republic of China
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Chen H, Zhou H, Sun T, Xu J, Tu Q, Yang J, Zhang Y, Bian X. Identification of Holrhizins E-Q Reveals the Diversity of Nonribosomal Lipopeptides in Paraburkholderia rhizoxinica. JOURNAL OF NATURAL PRODUCTS 2020; 83:537-541. [PMID: 32031805 DOI: 10.1021/acs.jnatprod.9b00927] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The products of a nonribosomal peptide synthetase gene, holA, from Paraburkholderia rhizoxinica were investigated using our recently established recombineering technique. Fifteen products, including 13 new linear lipopeptides, holrhizins E-Q (2-8, 10-15), together with the two known holrhizins A and B (1, 9), were detected in the activated mutant, and their structures were identified using HRESIMS, NMR spectroscopy, Marfey's analysis, and feeding experiments with labeled amino acids. The lipohexapeptides 1-3 and 7-14 differ in three amino acid residues and the N-terminal fatty acid chains. The diversity of the holrhizins originates from the substrate flexibility of the A4, A5, and A6 domains as well as the starter C domain in the biosynthetic pathway.
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Affiliation(s)
- Hanna Chen
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology , Shandong University , Qingdao , Shandong 266237 , People's Republic of China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology , Shandong University , Qingdao , Shandong 266237 , People's Republic of China
| | - Tao Sun
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology , Shandong University , Qingdao , Shandong 266237 , People's Republic of China
| | - Jiaying Xu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science , Hunan Normal University , Changsha , 410081 , People's Republic of China
| | - Qiang Tu
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology , Shandong University , Qingdao , Shandong 266237 , People's Republic of China
| | - Jie Yang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology , Shandong University , Qingdao , Shandong 266237 , People's Republic of China
- Jiangsu Marine Resources Development Research Institute , Lianyungang , 222005 , People's Republic of China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology , Shandong University , Qingdao , Shandong 266237 , People's Republic of China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology , Shandong University , Qingdao , Shandong 266237 , People's Republic of China
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Ouyang Q, Wang X, Zhang N, Zhong L, Liu J, Ding X, Zhang Y, Bian X. Promoter Screening Facilitates Heterologous Production of Complex Secondary Metabolites in Burkholderiales Strains. ACS Synth Biol 2020; 9:457-460. [PMID: 31999442 DOI: 10.1021/acssynbio.9b00459] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Burkholderiales are an emerging source of bioactive secondary metabolites and have the potential to be a robust chassis for metabolites from Gram-negative bacteria. However, only a few constitutive promoters can be utilized in Burkholderiales. Herein, we described the screening of strong constitutive promoters from Burkholderiales strain DSM 7029, and 37 promoters identified from transcriptome sequencing were cloned and characterized using a firefly luciferase reporter and were further verified by qPCR analysis. These promoters were then used to drive a complex 56-kb epothilone BGC from myxobacterium and a 23-kb rhizomide BGC from Paraburkholderia rhizoxinica, and the successful production of epothilone and rhizomide was observed in DSM 7029, with improved yields compared to the production achieved by previously used promoters. Additionally, these promoters are also functional in other Burkholderiales species. Thus, these promoters are highly useful for optimizing yields of important metabolites in Burkholderiales and for mining cryptic biosynthetic pathways in DSM 7029.
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Affiliation(s)
- Qing Ouyang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Na Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Lin Zhong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Jiaqi Liu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Xiaoming Ding
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
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Zhou XK, Li QQ, Dong LM, Yang DQ, Liu L, Fang BZ, Jeon CO, Li WJ, Duan YQ. Pseudorivibacter rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere soil of Camellia sinensis (L.) O. Ktze and emended description of the genus Rivibacter. Int J Syst Evol Microbiol 2019; 70:1071-1078. [PMID: 31755854 DOI: 10.1099/ijsem.0.003878] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, facultative anaerobic, motile and straight rod-shaped bacterium, designated strain C1-9T, was isolated from rhizosphere soil of Camellia sinensis (L.) O. Ktze collected from a tea garden in Huize, south-western PR China. Cells were oxidase-positive and catalase-negative. Growth occurred at 20-40 °C and pH 6.0-10.0, with an optimal growth at 30 °C and pH 7.0. The respiratory quinone was detected as ubiquinone-8 (Q-8). The major fatty acids were identified as summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c or C18 : 1ω6c). The cellular polar lipids contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids, two unidentified lipids, one unidentified aminophospholipid and one unidentified aminolipid. The polyamine types were detected as 1,8-diaminooctane and 2-hydroxyputrescine. The genomic DNA G+C content was 68.6 mol%. Based on the results of 16S rRNA gene sequence analysis, strain C1-9T (MF687442) showed highest sequence similarity to Rivibacter subsaxonicus DSM 19570T (97.1 %). The phylogenetic tree based on 16S rRNA gene sequences showed that strain C1-9T clustered close to R. subsaxonicus DSM 19570T, Methylibium petroleiphilum CCTCC AB 2014193T and species belonging to the genera Rhizobacter and Piscinibacter. The phylogenomic tree indicated that strain C1-9T formed a clade with R. subsaxonicus. The average nucleotide identity value was 76.0 % between strain C1-9T and R. subsaxonicus DSM 19570T, which is lower than the prokaryotic species delineation threshold of 95.0-96.0 %. The polyphasic taxonomic characteristics indicated that strain C1-9T represents a novel species of a new genus within the order Burkholderiales, for which the name Pseudorivibacter rhizosphaerae gen. nov., sp. nov. (type strain C1-9T = KCTC 62325T=CGMCC 1.13864T) is proposed.
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Affiliation(s)
- Xing-Kui Zhou
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, PR China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Qing-Qing Li
- Life Science College, Southwest Forestry University, Kunming 650224, PR China.,Key Laboratory for Conserving Wildlife with Small Populations in Yunnan (Southwest Forestry University), Kunming 650224, PR China
| | - Li-Min Dong
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, PR China
| | - Deng-Qiang Yang
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, PR China
| | - Lan Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Yan-Qing Duan
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, PR China
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