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Yang G, Li S, Ma Y, Peng S, Zeng X, Huang J, Deng A, Qiao S, Yu H. Construction of an efficient electroporation transformation system promotes the application of Targetron in wild-type Paenibacillus elgii 219. Appl Environ Microbiol 2025; 91:e0204124. [PMID: 40261057 DOI: 10.1128/aem.02041-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Accepted: 02/18/2025] [Indexed: 04/24/2025] Open
Abstract
Paenibacillus species have attracted much attention as a promising cell factory that can yield a variety of bioactive peptides and functional exopolysaccharides. Improving the production capacity of Paenibacillus through genetic engineering is crucial for the development of bioactive natural products. This study systematically evaluated the effects of electroporation transformation parameters on the introduction of DNA into Paenibacillus elgii 219, which was isolated from soil and preserved in our lab. The transformation efficiency was improved to 1.25 × 106 transformants/μg DNA by optimizing factors including the growth and recovery media content, the growth stages of P. elgii 219, electric field strength, electroporation buffer composition, cell wall weakening, and DNA quality. The results represent the highest transformation efficiency reported thus far for Paenibacillus. This work further established a group II intron-based gene editing system suitable for P. elgii 219 for the first time. As expected, plasmid pDX4383 was successfully transferred into P. elgii 219, and a putative glycosyltransferase gene was deleted, thereby eliminating flocculent precipitation during fermentation. Taken together, this study demonstrates that the electroporation-mediated transformation of exogenous DNA combined with group II intron-based gene editing provides an effective approach for the genetic engineering of Paenibacillus bacteria.IMPORTANCEThe establishment of an efficient plasmid DNA transformation protocol for P. elgii 219 has established a robust foundation for further in-depth investigations into its physiological and metabolic processes. Additionally, the successful advancement of group II intron-mediated gene editing technology imbues P. elgii 219 with the potential to serve as a highly efficient cell factory. These accomplishments furnish novel perspectives and references for the exploration of other Paenibacillus species in environmental contexts and the development of their products with economic value.
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Affiliation(s)
- Guangxin Yang
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture and Rural Affairs Feed Industry Centre, China Agricultural University, Beijing, China
- Frontier Technology Research Institute of China Agricultural University in Shenzhen, Shenzhen, China
| | - Siyu Li
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture and Rural Affairs Feed Industry Centre, China Agricultural University, Beijing, China
- Frontier Technology Research Institute of China Agricultural University in Shenzhen, Shenzhen, China
| | - Yonghang Ma
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture and Rural Affairs Feed Industry Centre, China Agricultural University, Beijing, China
- Frontier Technology Research Institute of China Agricultural University in Shenzhen, Shenzhen, China
| | - Siyi Peng
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture and Rural Affairs Feed Industry Centre, China Agricultural University, Beijing, China
- Frontier Technology Research Institute of China Agricultural University in Shenzhen, Shenzhen, China
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture and Rural Affairs Feed Industry Centre, China Agricultural University, Beijing, China
- Frontier Technology Research Institute of China Agricultural University in Shenzhen, Shenzhen, China
| | - Jinxiu Huang
- ChongQing Academy of Animal Sciences, Rongchang, Chongqing, China
- National Center of Technology Innovation for Pigs, Rongchang, Chongqing, China
| | - AiHua Deng
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture and Rural Affairs Feed Industry Centre, China Agricultural University, Beijing, China
- Frontier Technology Research Institute of China Agricultural University in Shenzhen, Shenzhen, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture and Rural Affairs Feed Industry Centre, China Agricultural University, Beijing, China
- Frontier Technology Research Institute of China Agricultural University in Shenzhen, Shenzhen, China
| | - Haitao Yu
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture and Rural Affairs Feed Industry Centre, China Agricultural University, Beijing, China
- Frontier Technology Research Institute of China Agricultural University in Shenzhen, Shenzhen, China
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Xu S, Liu Z, Ren P, Liu Y, Xiao F, Li W. BmfR, a novel GntR family regulator, regulates biofilm formation in marine-derived, Bacillus methylotrophicus B-9987. Microbiol Res 2024; 287:127859. [PMID: 39098095 DOI: 10.1016/j.micres.2024.127859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/21/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024]
Abstract
Biofilms are common living states for microorganisms, allowing them to adapt to environmental changes. Numerous Bacillus strains can form complex biofilms that play crucial roles in biocontrol processes. However, our current understanding of the molecular mechanisms of biofilm formation in Bacillus is mainly based on studies of Bacillus subtilis. Knowledge regarding the biofilm formation of other Bacillus species remains limited. In this study, we identified a novel transcriptional regulator, BmfR, belonging to the GntR family, that regulates biofilm formation in marine-derived Bacillus methylotrophicus B-9987. We demonstrated that BmfR induces biofilm formation by activating the extracellular polysaccharide structural genes epsA-O and negatively regulating the matrix gene repressor, SinR; of note it positively affects the expression of the master regulator of sporulation, Spo0A. Furthermore, database mining for BmfR homologs has revealed their widespread distribution among many bacterial species, mainly Firmicutes and Proteobacteria. This study advances our understanding of the biofilm regulatory network of Bacillus strains, and provides a new target for exploiting and manipulating biofilm formation.
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Affiliation(s)
- Shanshan Xu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Zengzhi Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Pengfei Ren
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yang Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Fei Xiao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shannxi 712100, China.
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Liu Y, Cheng H, Li H, Zhang Y, Wang M. A Programmable CRISPR/Cas9 Toolkit Improves Lycopene Production in Bacillus subtilis. Appl Environ Microbiol 2023; 89:e0023023. [PMID: 37272803 PMCID: PMC10305015 DOI: 10.1128/aem.00230-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/16/2023] [Indexed: 06/06/2023] Open
Abstract
Bacillus subtilis has been widely used and generally recognized as a safe host for the production of recombinant proteins, high-value chemicals, and pharmaceuticals. Thus, its metabolic engineering attracts significant attention. Nevertheless, the limited availability of selective markers makes this process difficult and time-consuming, especially in the case of multistep biosynthetic pathways. Here, we employ CRISPR/Cas9 technology to build an easy cloning toolkit that addresses commonly encountered obstacles in the metabolic engineering of B. subtilis, including the chromosomal integration locus, promoter, terminator, and guide RNA (gRNA) target. Six promoters were characterized, and the promoter strengths ranged from 0.9- to 23-fold that of the commonly used strong promoter P43. We characterized seven terminators in B. subtilis, and the termination efficiencies (TEs) of the seven terminators are all more than 90%. Six gRNA targets were designed upstream of the promoter and downstream of the terminator. Using a green fluorescent protein (GFP) reporter, we confirmed integration efficiency with the single-locus integration site is up to 100%. We demonstrated the applicability of this toolkit by optimizing the expression of a challenging but industrially important product, lycopene. By heterologous expression of the essential genes for lycopene synthesis on the B. subtilis genome, a total of 13 key genes involved in the lycopene biosynthetic pathway were manipulated. Moreover, our findings showed that the gene cluster ispG-idi-dxs-ispD could positively affect the production of lycopene, while the cluster dxr-ispE-ispF-ispH had a negative effect on lycopene production. Hence, our multilocus integration strategy can facilitate the pathway assembly for production of complex chemicals and pharmaceuticals in B. subtilis. IMPORTANCE We present a toolkit that allows for rapid cloning procedures and one-step subcloning to move from plasmid-based expression to stable chromosome integration and expression in a production strain in less than a week. The utility of the customized tool was demonstrated by integrating the MEP (2C-methyl-d-erythritol-4-phosphate) pathway, part of the pentose phosphate pathway (PPP), and the hetero-lycopene biosynthesis genes by stable expression in the genome. The tool could be useful to engineer B. subtilis strains through diverse recombination events and ultimately improve its potential and scope of industrial application as biological chassis.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Haijiao Cheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Haoni Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yingzhe Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Meng Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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Ondzighi‐Assoume CA, Bhusal B, Traore AM, Ouma WK, Mmbaga MT, Swiggart EM. Efficient fluorescence-based localization technique for real-time tracking endophytes route in host-plants colonization. PLANT DIRECT 2022; 6:e427. [PMID: 35959216 PMCID: PMC9360559 DOI: 10.1002/pld3.427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 06/01/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Bacterial isolates that enhance plant growth and suppress plant pathogens growth are essential tools for reducing pesticide applications in plant production systems. The objectives of this study were to develop a reliable fluorescence-based technique for labeling bacterial isolates selected as biological control agents (BCAs) to allow their direct tracking in the host-plant interactions, understand the BCA localization within their host plants, and the route of plant colonization. Objectives were achieved by developing competent BCAs transformed with two plasmids, pBSU101 and pANIC-10A, containing reporter genes eGFP and pporRFP, respectively. Our results revealed that the plasmid-mediated transformation efficiencies of antibiotic-resistant competent BCAs identified as PSL, IMC8, and PS were up 84%. Fluorescent BCA-tagged reporter genes were associated with roots and hypocotyls but not with leaves or stems and were confirmed by fluoresence microscopy and PCR analyses in colonized Arabidopsis and sorghum. This fluorescence-based technique's high resolution and reproducibility make it a platform-independent system that allows tracking of BCAs spatially within plant tissues, enabling assessment of the movement and niches of BCAs within colonized plants. Steps for producing and transforming competent fluorescent BCAs, as well as the inoculation of plants with transformed BCAs, localization, and confirmation of fluorescent BCAs through fluorescence imaging and PCR, are provided in this manuscript. This study features host-plant interactions and subsequently biological and physiological mechanisms implicated in these interactions. The maximum time to complete all the steps of this protocol is approximately 3 months.
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Affiliation(s)
- Christine A. Ondzighi‐Assoume
- College of Agriculture, Department of Agricultural and Environmental SciencesTennessee State UniversityNashvilleTennesseeUSA
| | - Bandana Bhusal
- College of Agriculture, Department of Agricultural and Environmental SciencesTennessee State UniversityNashvilleTennesseeUSA
| | - Adam M. Traore
- College of Agriculture, Department of Agricultural and Environmental SciencesTennessee State UniversityNashvilleTennesseeUSA
| | - Wilson K. Ouma
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTennesseeUSA
| | - Margaret T. Mmbaga
- College of Agriculture, Department of Agricultural and Environmental SciencesTennessee State UniversityNashvilleTennesseeUSA
| | - Ethan M. Swiggart
- College of Agriculture, Department of Agricultural and Environmental SciencesTennessee State UniversityNashvilleTennesseeUSA
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5
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Wu T, Xiao F, Li W. Macrolactins: biological activity and biosynthesis. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:62-68. [PMID: 37073393 PMCID: PMC10064405 DOI: 10.1007/s42995-020-00068-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/03/2020] [Indexed: 05/03/2023]
Abstract
Marine microorganisms have proven to be a rich source of natural products with unique structures and novel activities, due to their special living conditions. Macrolactins (MLNs), mostly produced by marine-derived microorganisms, are a group of 24-membered lactone natural products, which exhibit potent antibacterial, antifungal, antiviral, anticancer, anti-inflammatory, anti-angiogenic and other activities. Their extensive biological activities make them potential compounds for drug development. MLNs are biosynthesized via a type I polyketide synthase (PKS) pathway with different tailoring steps, such as epoxidation, glycosylation and acylation. These modification steps provide opportunities to diversify their structures by combinatorial biosynthesis strategies. This review mainly focuses on the newly discovered MLNs in the past five years, including their biological activities and relevant biosynthetic studies.
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Affiliation(s)
- Ting Wu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
| | - Fei Xiao
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
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6
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In-situ generation of large numbers of genetic combinations for metabolic reprogramming via CRISPR-guided base editing. Nat Commun 2021; 12:678. [PMID: 33514753 PMCID: PMC7846839 DOI: 10.1038/s41467-021-21003-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 01/07/2021] [Indexed: 11/09/2022] Open
Abstract
Reprogramming complex cellular metabolism requires simultaneous regulation of multigene expression. Ex-situ cloning-based methods are commonly used, but the target gene number and combinatorial library size are severely limited by cloning and transformation efficiencies. In-situ methods such as multiplex automated genome engineering (MAGE) depends on high-efficiency transformation and incorporation of heterologous DNA donors, which are limited to few microorganisms. Here, we describe a Base Editor-Targeted and Template-free Expression Regulation (BETTER) method for simultaneously diversifying multigene expression. BETTER repurposes CRISPR-guided base editors and in-situ generates large numbers of genetic combinations of diverse ribosome binding sites, 5’ untranslated regions, or promoters, without library construction, transformation, and incorporation of DNA donors. We apply BETTER to simultaneously regulate expression of up to ten genes in industrial and model microorganisms Corynebacterium glutamicum and Bacillus subtilis. Variants with improved xylose catabolism, glycerol catabolism, or lycopene biosynthesis are respectively obtained. This technology will be useful for large-scale fine-tuning of multigene expression in both genetically tractable and intractable microorganisms. To obtain optimal yield and productivity in bioproduction, expression of pathway genes must be appropriately coordinated. Here, the authors report repurposing of base editors for simultaneous regulation of multiple gene expression and demonstrate its application in industrially important and model microorganisms.
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Li H, Han X, Dong Y, Xu S, Chen C, Feng Y, Cui Q, Li W. Bacillaenes: Decomposition Trigger Point and Biofilm Enhancement in Bacillus. ACS OMEGA 2021; 6:1093-1098. [PMID: 33490768 PMCID: PMC7818078 DOI: 10.1021/acsomega.0c03389] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/19/2020] [Indexed: 06/12/2023]
Abstract
Bacillaenes are a class of poly-unsaturated enamines produced by Bacillus strains that are notoriously unstable toward light, oxygen, and normal temperature. Herein, in an in-depth study of this highly unstable chemotype, the stability and biological function of bacillaenes were investigated. The structure change of the bacillaene scaffold was tracked by time-course 1H NMR data analysis coupled with the differential analysis of 2D-NMR spectra method, which was demonstrated to be a "domino" effect triggered by 4',5'-cis (2 and 3) configuration rearranged to trans (2a and 3a). These findings provide the possibility for stabilizing the bacillaene scaffold by chemical modification of its trigger points. In the biofilm assay, compounds 1 and 2 accelerated self-biofilm formation in Bacillus methylotrophicus B-9987 at low concentrations of 1.0 and 0.1 μg/mL. Interestingly, bacillaenes play dual roles as antibiotic and biofilm enhancers in a dose-dependent manner, both of which serve in the self-protection of Bacillus.
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Affiliation(s)
- Huayue Li
- Key
Laboratory of Marine Drugs, Ministry of Education, School of Medicine
and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory
for Marine Drugs and Bioproducts of Qingdao National Laboratory for
Marine Science and Technology, Qingdao 266237, China
| | - Xiao Han
- Key
Laboratory of Marine Drugs, Ministry of Education, School of Medicine
and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yujing Dong
- Key
Laboratory of Marine Drugs, Ministry of Education, School of Medicine
and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Shanshan Xu
- Key
Laboratory of Marine Drugs, Ministry of Education, School of Medicine
and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Chao Chen
- Shandong
Provincial Key Laboratory of Energy Genetics, Qingdao Institute of
Bioenergy and Bioprocess Technology, Chinese
Academy of Sciences, Qingdao 266101, China
- Key
Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess
Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao
Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy
of Sciences, Qingdao 266101, China
| | - Yingang Feng
- Shandong
Provincial Key Laboratory of Energy Genetics, Qingdao Institute of
Bioenergy and Bioprocess Technology, Chinese
Academy of Sciences, Qingdao 266101, China
- Key
Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess
Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao
Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy
of Sciences, Qingdao 266101, China
| | - Qiu Cui
- Shandong
Provincial Key Laboratory of Energy Genetics, Qingdao Institute of
Bioenergy and Bioprocess Technology, Chinese
Academy of Sciences, Qingdao 266101, China
- Key
Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess
Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao
Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy
of Sciences, Qingdao 266101, China
| | - Wenli Li
- Key
Laboratory of Marine Drugs, Ministry of Education, School of Medicine
and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory
for Marine Drugs and Bioproducts of Qingdao National Laboratory for
Marine Science and Technology, Qingdao 266237, China
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Li H, Han X, Zhang J, Dong Y, Xu S, Bao Y, Chen C, Feng Y, Cui Q, Li W. An Effective Strategy for Identification of Highly Unstable Bacillaenes. JOURNAL OF NATURAL PRODUCTS 2019; 82:3340-3346. [PMID: 31773959 DOI: 10.1021/acs.jnatprod.9b00609] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Exploration of unstable compounds is a rarely explored area of natural product research. We describe the integration of genomic and metabolomic analyses with bioassay-guided compound mining to effectively explore unstable bacillaenes. New bacillaene structures (2, 4, and 5) were identified from compound mixtures using the DANS-SVI (differential analysis of 2D NMR spectrum-single spectrum with variable intensities) method, which were further verified by the isolation of the pure compounds under strictly controlled conditions. Compound 1 exhibited antibacterial activity against multi-drug-resistant bacterial strains, while glycosylation decreased the activity of the bacillaene scaffold.
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Affiliation(s)
- Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 , China
| | - Xiao Han
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , China
| | - Jun Zhang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , China
| | - Yujing Dong
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , China
| | - Shanshan Xu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , China
| | - Yilei Bao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , China
| | - Chao Chen
- Shandong Provincial Key Laboratory of Energy Genetics , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266101 , China
- Key Laboratory of Biofuels , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266101 , China
- Qingdao Engineering Laboratory of Single Cell Oil , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266101 , China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266101 , China
- Key Laboratory of Biofuels , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266101 , China
- Qingdao Engineering Laboratory of Single Cell Oil , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266101 , China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266101 , China
- Key Laboratory of Biofuels , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266101 , China
- Qingdao Engineering Laboratory of Single Cell Oil , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266101 , China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 , China
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Kaspar F, Neubauer P, Gimpel M. Bioactive Secondary Metabolites from Bacillus subtilis: A Comprehensive Review. JOURNAL OF NATURAL PRODUCTS 2019; 82:2038-2053. [PMID: 31287310 DOI: 10.1021/acs.jnatprod.9b00110] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacillus subtilis is widely underappreciated for its inherent biosynthetic potential. This report comprehensively summarizes the known bioactive secondary metabolites from B. subtilis and highlights potential applications as plant pathogen control agents, drugs, and biosurfactants. B. subtilis is well known for the production of cyclic lipopeptides exhibiting strong surfactant and antimicrobial activities, such as surfactins, iturins, and fengycins. Several polyketide-derived macrolides as well as nonribosomal peptides, dihydroisocoumarins, and linear lipopeptides with antimicrobial properties have been reported, demonstrating the biosynthetic arsenal of this bacterium. Promising efforts toward the application of B. subtilis strains and their natural products in areas of agriculture and medicine are underway. However, industrial-scale availability of these compounds is currently limited by low fermentation yields and challenging accessibility via synthesis, necessitating the development of genetically engineered strains and optimized cultivation processes. We hope that this review will attract renewed interest in this often-overlooked bacterium and its impressive biosynthetic skill set.
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Affiliation(s)
- Felix Kaspar
- Institute of Biotechnology , Technical University of Berlin , Ackerstraße 76 , 13355 Berlin , Germany
| | - Peter Neubauer
- Institute of Biotechnology , Technical University of Berlin , Ackerstraße 76 , 13355 Berlin , Germany
| | - Matthias Gimpel
- Institute of Biotechnology , Technical University of Berlin , Ackerstraße 76 , 13355 Berlin , Germany
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10
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Mahipant G, Kato J, Kataoka N, Vangnai AS. An alternative genome-integrated method for undomesticated Bacillus subtilis and related species. J GEN APPL MICROBIOL 2019; 65:96-105. [PMID: 30487367 DOI: 10.2323/jgam.2018.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Given their applicability in genetic engineering, undomesticated Bacillus strains are extensively used as non-natural hosts for chemical production due to their high tolerance of toxic substrates or products. However, they are difficult to genomically modify due to their low transformation efficiencies. In this study, the Bacillus-E. coli shuttle vector pHY300PLK, which is widely used in gram-positive bacteria, was adopted for genome integration in organic solvent-tolerant Bacillus isolates. The Bacillus-replicative vector was used to deliver homologous recombinant DNA and propagate itself inside the host cell, increasing the likelihood of genome integration of the recombinant DNA. Then, the unintegrated vectors were cured by cell cultivation in antibiotic-free medium with facilitation of nickel ions. The developed protocol was successfully demonstrated and validated by the disruption of amyE gene in B. subtilis 168. With an improved clonal selection protocol, the probability of clonal selection of the amyE::cat genome-integrated mutants was increased up to 42.0 ± 10.2%. Genome integration in undomesticated, organic solvent tolerant Bacillus strains was also successfully demonstrated with amyE as well as proB gene creating the gene-disrupted mutants with the corresponding phenotype and genotype. Not only was this technique effectively applied to several strains of undomesticated B. subtilis, but it was also successfully applied to B. cereus. This study validates the possibility of the application of Bacillus-replicative vector as well as the developed protocol in a variety of genome modification of undomesticated Bacillus species.
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Affiliation(s)
- Gumpanat Mahipant
- Biological Sciences Program, Faculty of Science, Chulalongkorn University.,Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University
| | - Junichi Kato
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University
| | - Naoya Kataoka
- Division of Agricultural Sciences, Graduate School of Sciences and Technology for Innovation, Yamaguchi University.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University
| | - Alisa S Vangnai
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University.,Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University
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11
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Zeaiter Z, Mapelli F, Crotti E, Borin S. Methods for the genetic manipulation of marine bacteria. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Wu L, Guo X, Liu X, Yang H. NprR-NprX Quorum-Sensing System Regulates the Algicidal Activity of Bacillus sp. Strain S51107 against Bloom-Forming Cyanobacterium Microcystis aeruginosa. Front Microbiol 2017; 8:1968. [PMID: 29075240 PMCID: PMC5641580 DOI: 10.3389/fmicb.2017.01968] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/25/2017] [Indexed: 11/24/2022] Open
Abstract
Harmful cyanobacterial blooms have severely impaired freshwater quality and threatened human health worldwide. Here, a Gram-positive bacterium, Bacillus sp. strain S51107, which exhibits strong algicidal activity against Microcystis aeruginosa, was isolated from Lake Taihu. We found that the algicidal activity of strain S51107 was regulated primarily by NprR-NprX quorum sensing (QS), in which the mature form of the signaling peptide NprX was identified as the SKPDIVG heptapeptide. Disruption of the nprR-nprX cassette markedly decreased the algicidal activity, and complemented strains showed significantly recovered algicidal activity. Strain S51107 produced low-molecular-weight algicidal compounds [indole-3-carboxaldehyde and cyclo(Pro-Phe)] and high-molecular-weight algicidal substance(s) (>3 kDa). Moreover, the production of high-molecular-weight algicidal substance(s) was regulated by NprR-NprX QS, but the production of low-molecular-weight algicidal compounds was not. High-molecular-weight algicidal substance(s) played a more important role than low-molecular-weight algicidal compounds in the algicidal activity of strain S51107. The results of this study could increase our knowledge about algicidal characteristics of a potential algicidal bacterium, Bacillus sp. strain S51107, and provide the first evidence that the algicidal activity of Gram-positive algicidal bacteria is regulated by QS, which will greatly enhance our understanding of the interactions between algae and indigenous algicidal bacteria, thereby providing aid in the design and optimization of strategies to control harmful algae blooms.
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Affiliation(s)
- Lishuang Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xingliang Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xianglong Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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How to transform a recalcitrant Paenibacillus strain: From culture medium to restriction barrier. J Microbiol Methods 2016; 131:135-143. [PMID: 27780731 DOI: 10.1016/j.mimet.2016.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/11/2016] [Accepted: 10/21/2016] [Indexed: 11/20/2022]
Abstract
Paenibacillus riograndensis SBR5T is a plant growth-promoting bacterium isolated from the wheat rhizosphere. Its recalcitrance to genetic manipulation is a major bottleneck for molecular studies, as has been reported for other Paenibacillus environmental isolates. An efficient electroporation protocol was established by evaluating diverse parameters and optimizing the culture medium, culture growth phase, electroporation solution, recovery medium, DNA input, and electric field strength. Efficiencies of approximately 2.8×104transformantsμg-1 of plasmid DNA were obtained. The optimized protocol was tested with other Paenibacillus species, and the relevance of bypassing the restriction DNA defense system to transform Paenibacillus was highlighted. This protocol is the tool needed to deepen molecular studies with this strain and will aid in the manipulation of other new environmental isolates that also exhibit recalcitrant transformation difficulties.
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Liu Y, Qin W, Liu Q, Zhang J, Li H, Xu S, Ren P, Tian L, Li W. Genome-wide identification and characterization of macrolide glycosyltransferases from a marine-derived Bacillus strain and their phylogenetic distribution. Environ Microbiol 2016; 18:4770-4781. [PMID: 27130432 DOI: 10.1111/1462-2920.13367] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 04/25/2016] [Indexed: 11/30/2022]
Abstract
Clarifying glycosyltrasferases (GTs) function is of significance for the development of GT inhibitors as drugs, and the use of GTs to glycodiversify small molecules in the search of drug leads. While many Actinomyces natural-product GTs had been functionally characterized, our understanding towards Bacillus natural-product GTs is so far very limited. Herein, genome-wide identification of macrolide GT genes from marine-derived Bacillus methylotrophicus B-9987 revealed the presence of three macrolide GT genes bmmGT1-3. While bmmGT1 was previously revealed to be involved in the biosynthesis of trans-acyltransferase (AT) polyketides compounds macrolactins (MLNs) and bacillaenes (BAEs), the functions of bmmGT2 and bmmGT3 were probed, demonstrating that they are capable to biochemically catalyze glycosylation of MLNs and BAEs as well but interestingly with different regioselectivity, affording four new MLNs analogs. Notably, further genome mining revealed that the orthologs of these three macrolide GT genes showed a regular distribution in the subtilis- and the cereus-clade Bacillus strains; interestingly, bmmGT1 orthologs only occurred in the subtilis-clade Bacillus, and they were also found in the genomes of Streptomyces strains, suggesting their close phylogenetic relationship. These results provide the first significant insight into the important roles of Bacillus macrolide GTs in the biology of the species.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Wen Qin
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Quanquan Liu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Jun Zhang
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Shanshan Xu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Pengfei Ren
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Li Tian
- First Institute of Oceanography, State Oceanic Administration, 6 Xianxialing Road Qingdao, SD, 266061, P. R. China.,Qingdao University of Science & Technology, 53 Zhen Zhou Road Qingdao, SD, 266042, P. R. China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
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Qin W, Liu Y, Ren P, Zhang J, Li H, Tian L, Li W. Uncovering a Glycosyltransferase Provides Insights into the Glycosylation Step during Macrolactin and Bacillaene Biosynthesis. Chembiochem 2014; 15:2747-53. [DOI: 10.1002/cbic.201402384] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Indexed: 02/06/2023]
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