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Kan J, Morales A, Hernandez Y, Ternei MA, Lemetre C, Maclntyre LW, Biais N, Brady SF. Oxydifficidin, a potent Neisseria gonorrhoeae antibiotic due to DedA assisted uptake and ribosomal protein RplL sensitivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.596031. [PMID: 38854004 PMCID: PMC11160649 DOI: 10.1101/2024.05.27.596031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Gonorrhea, which is caused by Neisseria gonorrhoeae, is the second most prevalent sexually transmitted infection worldwide. The increasing appearance of isolates that are resistant to approved therapeutics raises the concern that gonorrhea may become untreatable. Here, we serendipitously identified oxydifficidin as a potent N. gonorrhoeae antibiotic through the observation of a Bacillus amyloliquefaciens contaminant in a lawn of N. gonorrhoeae. Oxydifficidin is active against both wild-type and multidrug-resistant N. gonorrhoeae. It's potent activity results from a combination of DedA-assisted uptake into the cytoplasm and the presence of an oxydifficidin-sensitive ribosomal protein L7/L12 (RplL). Our data indicates that oxydifficidin binds to the ribosome at a site that is distinct from other antibiotics and that L7/L12 is uniquely associated with its mode of action. This study opens a potential new avenue for addressing antibiotic resistant gonorrhea and underscores the possibility of identifying overlooked natural products from cultured bacteria, particularly those with activity against previously understudied pathogens.
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Affiliation(s)
- Jingbo Kan
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
- Graduate Center, City University of New York, New York, NY 10016
- Brooklyn College, City University of New York, Brooklyn, NY 11210
| | - Adrian Morales
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Yozen Hernandez
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Melinda A. Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Christophe Lemetre
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Logan W. Maclntyre
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Nicolas Biais
- Graduate Center, City University of New York, New York, NY 10016
- Brooklyn College, City University of New York, Brooklyn, NY 11210
- Laboratoire Jean Perrin, UMR 8237 Sorbonne Université/CNRS, Paris, France
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
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2
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Kim EYS, Maltempi de Souza E, Müller-Santos M. Optimisation of DNA electroporation protocols for different plant-associated bacteria. J Microbiol Methods 2024; 220:106912. [PMID: 38452904 DOI: 10.1016/j.mimet.2024.106912] [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: 12/19/2023] [Revised: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Electroporation is a vital process that facilitates the use of modern recombineering and other high-throughput techniques in a wide array of microorganisms, including non-model bacteria like plant growth-promoting bacteria (PGPB). These microorganisms play a significant role in plant health by colonizing plants and promoting growth through nutrient exchange and hormonal regulation. In this study, we introduce a sequential Design of Experiments (DOE) approach to obtain highly competent cells swiftly and reliably for electroporation. Our method focuses on optimizing the three stages of the electroporation procedure-preparing competent cells, applying the electric pulse field, and recovering transformed cells-separately. We utilized a split-plot fractional design with five factors and a covariate to optimize the first step, response surface methodology (RSM) for the second step, and Plackett-Burman design for two categorical factors and one continuous factor for the final step. Following the experimental sequence with three bacterial models, we achieved efficiencies 10 to 100 times higher, reaching orders of 105 to 106 CFU/μg of circular plasmid DNA. These results highlight the significant potential for enhancing electroporation protocols for non-model bacteria.
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Affiliation(s)
- Edson Yu Sin Kim
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Emanuel Maltempi de Souza
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Marcelo Müller-Santos
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil.
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3
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Tripathi S, Voogdt CGP, Bassler SO, Anderson M, Huang PH, Sakenova N, Capraz T, Jain S, Koumoutsi A, Bravo AM, Trotter V, Zimmerman M, Sonnenburg JL, Buie C, Typas A, Deutschbauer AM, Shiver AL, Huang KC. Randomly barcoded transposon mutant libraries for gut commensals I: Strategies for efficient library construction. Cell Rep 2024; 43:113517. [PMID: 38142397 DOI: 10.1016/j.celrep.2023.113517] [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: 07/27/2023] [Revised: 10/22/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
Randomly barcoded transposon mutant libraries are powerful tools for studying gene function and organization, assessing gene essentiality and pathways, discovering potential therapeutic targets, and understanding the physiology of gut bacteria and their interactions with the host. However, construction of high-quality libraries with uniform representation can be challenging. In this review, we survey various strategies for barcoded library construction, including transposition systems, methods of transposon delivery, optimal library size, and transconjugant selection schemes. We discuss the advantages and limitations of each approach, as well as factors to consider when selecting a strategy. In addition, we highlight experimental and computational advances in arraying condensed libraries from mutant pools. We focus on examples of successful library construction in gut bacteria and their application to gene function studies and drug discovery. Given the need for understanding gene function and organization in gut bacteria, we provide a comprehensive guide for researchers to construct randomly barcoded transposon mutant libraries.
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Affiliation(s)
- Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carlos Geert Pieter Voogdt
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Stefan Oliver Bassler
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany
| | - Mary Anderson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Po-Hsun Huang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nazgul Sakenova
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tümay Capraz
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Alexandra Koumoutsi
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Afonso Martins Bravo
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Valentine Trotter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael Zimmerman
- Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Justin L Sonnenburg
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cullen Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Athanasios Typas
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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4
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Marsh JW, Kirk C, Ley RE. Toward Microbiome Engineering: Expanding the Repertoire of Genetically Tractable Members of the Human Gut Microbiome. Annu Rev Microbiol 2023; 77:427-449. [PMID: 37339736 DOI: 10.1146/annurev-micro-032421-112304] [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] [Indexed: 06/22/2023]
Abstract
Genetic manipulation is necessary to interrogate the functions of microbes in their environments, such as the human gut microbiome. Yet, the vast majority of human gut microbiome species are not genetically tractable. Here, we review the hurdles to seizing genetic control of more species. We address the barriers preventing the application of genetic techniques to gut microbes and report on genetic systems currently under development. While methods aimed at genetically transforming many species simultaneously in situ show promise, they are unable to overcome many of the same challenges that exist for individual microbes. Unless a major conceptual breakthrough emerges, the genetic tractability of the microbiome will remain an arduous task. Increasing the list of genetically tractable organisms from the human gut remains one of the highest priorities for microbiome research and will provide the foundation for microbiome engineering.
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Affiliation(s)
- James W Marsh
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Christian Kirk
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
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Feng RY, Chen YH, Lin C, Tsai CH, Yang YL, Chen YL. Surfactin secreted by Bacillus amyloliquefaciens Ba01 is required to combat Streptomyces scabies causing potato common scab. FRONTIERS IN PLANT SCIENCE 2022; 13:998707. [PMID: 36388520 PMCID: PMC9664162 DOI: 10.3389/fpls.2022.998707] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Potato common scab, which is mainly caused by the bacterium Streptomyces scabies, occurs in key potato growing regions worldwide. It causes necrotic or corky symptoms on potato tubers and decreases the economic value of potato. At present, there is no recommended chemical or biological control for combating potato common scab in Taiwan. It can only reduce the occurrence by cultivation control, but the efficacy is limited. Previously we found that Bacillus amyloliquefaciens Ba01 could control potato common scab in pot assay and in the field. The potential anti-S. scabies mechanism was associated with surfactin secretion, but further molecular dissection was not conducted. Thus, in this study we aimed to determine whether surfactin is the main compound active against S. scabies by knocking out the srf gene cluster in Ba01. The cloning plasmid pRY1 was transformed to Ba01 by electroporation for in-frame deletion. Two independent Δsrf mutants were obtained and confirmed by specific primers and mass spectrometry. The swarming ability and S. scabies inhibition was significantly decreased (P<0.001) in Δsrf mutants. The swarming ability of Δsrf mutants could be restored by the addition of surfactin. Furthermore, we found that Ba01 formed wrinkled biofilm in MSgg liquid medium, while Δsrf mutants formed biofilm abnormally. Furthermore, the α-amylase, protease and phosphate-solubilizing ability of Δsrf mutants was decreased, and the mutants could not inhibit the growth and sporulation of S. scabies on potato tuber slices. In conclusion, srf gene cluster of B. amyloliquefaciens Ba01 is responsible for the secretion of surfactin and inhibition of S. scabies.
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Affiliation(s)
- Ru-Ying Feng
- Master Program for Plant Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Hsuan Chen
- Master Program for Plant Medicine, National Taiwan University, Taipei, Taiwan
| | - Chih Lin
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Chia-Hsin Tsai
- Plant Pathology Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ying-Lien Chen
- Master Program for Plant Medicine, National Taiwan University, Taipei, Taiwan
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
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6
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Xin Q, Wang B, Pan L. Development and application of a CRISPR-dCpf1 assisted multiplex gene regulation system in Bacillus amyloliquefaciens LB1ba02. Microbiol Res 2022; 263:127131. [PMID: 35868259 DOI: 10.1016/j.micres.2022.127131] [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: 06/07/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 10/17/2022]
Abstract
Bacillus amyloliquefaciens LB1ba02 is generally recognized as food safe (GRAS) microbial host and important enzyme-producing strain in the industry. However, the restriction-modification system, existed in B. amyloliquefaciens LB1ba02, results in a low transformation efficiency, which makes its CRISPR tool development lagging far behind other Bacillus species. Here, we adapted a nuclease-deficient mutant dCpf1 (D917A) of Cpf1 and developed a CRISPR/dCpf1 assisted multiplex gene regulation system for the first time in B. amyloliquefaciens LB1ba02. A 73.9-fold inhibition efficiency and an optimal 1.8-fold activation effect at the - 327 bp site upstream of the TSS were observed in this system. In addition, this system achieved the simultaneous activation of the expression of three genes (secE, secDF, and prsA) by designing a crRNA array. On this basis, we constructed a crRNA activation library for the proteins involved in the Sec pathway, and screened 7 proteins that could promote the secretion of extracellular proteins. Among them, the most significant effect was observed when the expression of molecular motor transporter SecA was activated. Not only that, we constructed crRNA arrays to activate the expression of two or three proteins in combination. The results showed that the secretion efficiency of fluorescent protein GFP was further increased and an optimal 9.8-fold effect was observed when SecA and CsaA were simultaneously activated in shake flask fermentation. Therefore, the CRISPR/dCpf1-ω transcription regulation system can be applied well in a restriction-modification system strain and this system provides another CRISPR-based regulation tool for researchers who are committed to the development of genetic engineering and metabolic circuits in B. amyloliquefaciens.
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Affiliation(s)
- Qinglong Xin
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Panyu District, Guangzhou 510006, Guangdong, PR China
| | - Bin Wang
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Panyu District, Guangzhou 510006, Guangdong, PR China.
| | - Li Pan
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Panyu District, Guangzhou 510006, Guangdong, PR China.
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7
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Ma Y, Qiu Y, Yu C, Li S, Xu H. Design and construction of a Bacillus amyloliquefaciens cell factory for hyaluronic acid synthesis from Jerusalem artichoke inulin. Int J Biol Macromol 2022; 205:410-418. [PMID: 35202630 DOI: 10.1016/j.ijbiomac.2022.02.100] [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: 09/26/2021] [Revised: 01/21/2022] [Accepted: 02/16/2022] [Indexed: 11/05/2022]
Abstract
Hyaluronic acid (HA), a high-value biomacromolecule, has wide applications in medical, cosmetic and food fields. Currently, employing the safe-grade microorganisms for de novo biosynthesis of HA from renewable substrates has become a promising alternative. In this study, we established a Bacillus amyloliquefaciens strain as platform for HA production from Jerusalem artichoke inulin. Firstly, the different HA and UDP-GlcUA synthase genes were introduced into B. amyloliquefaciens to construct the HA synthesis pathway. Secondly, the byproduct polysaccharides were removed by knocking sacB and epsA-O using CRISPR/Cas9n system, resulting in a 13% increase in HA production. Finally, 2.89 g/L HA with a high molecular weight of 1.5 MDa was obtained after optimizing fermentation conditions and adding osmotic agents. This study demonstrates the engineered B. amyloliquefaciens can effectively synthesize HA with Jerusalem artichoke inulin and provides a green route for HA production.
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Affiliation(s)
- Yanqin Ma
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Yibin Qiu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, PR China; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, PR China
| | - Caiyuan Yu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Sha Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China.
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China.
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8
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Agostini F, Vicinanza C, Biolo G, Spessotto P, Da Ros F, Lombardi E, Durante C, Mazzucato M. Nucleofection of Adipose Mesenchymal Stem/Stromal Cells: Improved Transfection Efficiency for GMP Grade Applications. Cells 2021; 10:cells10123412. [PMID: 34943920 PMCID: PMC8700287 DOI: 10.3390/cells10123412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 12/19/2022] Open
Abstract
Nucleofection (NF) is a safe, non-viral transfection method, compatible with Good Manufacturing Practice guidelines. Such a technique is useful to improve therapeutic effectiveness of adipose tissue mesenchymal stem cells (ASC) in clinical settings, but improvement of NF efficiency is mandatory. Supernatant rich in growth factors (SRGF) is a clinical-grade medium additive for ASC expansion. We showed a dramatically increased NF efficiency and post-transfection viability in ASC expanded in presence of SRGF (vs. fetal bovine serum). SRGF expanded ASC were characterized by increased vesicle endocytosis but lower phagocytosis properties. SRGF increased n-6/n-3 ratio, reduced membrane lipid raft occurrence, and lowered intracellular actin content in ASC. A statistical correlation between NF efficiency and lipid raft availability on cell membranes was shown, even though a direct relationship could not be demonstrated: attempts to selectively modulate lipid rafts levels were, in fact, limited by technical constraints. In conclusion, we reported for the first time that tuning clinical-grade compatible cell culture conditions can significantly improve ASC transfection efficiency by a non-viral and safe approach. A deep mechanistic characterization is extremely complex, but we can hypothesize that integrated changes in membrane structure and intracellular actin content could contribute to explain SRGF impact on ASC NF efficiency.
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Affiliation(s)
- Francesco Agostini
- Stem Cell Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy; (C.V.); (F.D.R.); (E.L.); (C.D.); (M.M.)
- Correspondence: ; Tel.: +39-0434-659095
| | - Carla Vicinanza
- Stem Cell Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy; (C.V.); (F.D.R.); (E.L.); (C.D.); (M.M.)
| | - Gianni Biolo
- Unit of Internal Medicine, Clinica Medica, Department of Medical Surgical and Health Sciences, University of Trieste, Strada di Fiume 447, 34100 Trieste, Italy;
| | - Paola Spessotto
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy;
| | - Francesco Da Ros
- Stem Cell Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy; (C.V.); (F.D.R.); (E.L.); (C.D.); (M.M.)
| | - Elisabetta Lombardi
- Stem Cell Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy; (C.V.); (F.D.R.); (E.L.); (C.D.); (M.M.)
| | - Cristina Durante
- Stem Cell Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy; (C.V.); (F.D.R.); (E.L.); (C.D.); (M.M.)
| | - Mario Mazzucato
- Stem Cell Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy; (C.V.); (F.D.R.); (E.L.); (C.D.); (M.M.)
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9
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He P, Li S, Xu S, Fan H, Wang Y, Zhou W, Fu G, Han G, Wang YY, Zheng SJ. Monitoring Tritrophic Biocontrol Interactions Between Bacillus spp., Fusarium oxysporum f. sp. cubense, Tropical Race 4, and Banana Plants in vivo Based on Fluorescent Transformation System. Front Microbiol 2021; 12:754918. [PMID: 34721361 PMCID: PMC8550332 DOI: 10.3389/fmicb.2021.754918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/22/2021] [Indexed: 11/27/2022] Open
Abstract
Bacillus spp. is effective biocontrol agents for Fusarium wilt of banana (FWB), tropical race 4 (TR4). This study explores the colonization by Bacillus subtilis, Bacillus velezensis, and Bacillus amyloliquefaciens of host banana plants and elucidates the mechanism of antagonistic TR4 biocontrol. The authors selected one B. subtilis strain, three B. velezensis strains, and three B. amyloliquefaciens strains that are proven to significantly inhibit TR4 in vitro, optimized the genetic transformation conditions and explored their colonization process in banana plants. The results showed that we successfully constructed an optimized fluorescent electro-transformation system (OD600 of bacteria concentration=0.7, plasmid concentration=50ng/μl, plasmid volume=2μl, transformation voltage=1.8kV, and transformation capacitance=400Ω) of TR4-inhibitory Bacillus spp. strains. The red fluorescent protein (RFP)-labeled strains were shown to have high stability with a plasmid-retention frequency above 98%, where bacterial growth rates and TR4 inhibition are unaffected by fluorescent plasmid insertion. In vivo colonizing observation by Laser Scanning Confocal Microscopy (LSCM) and Scanning Electron Microscopy (SEM) showed that Bacillus spp. can colonize the internal cells of banana plantlets roots. Further, fluorescent observation by LSCM showed these RFP-labeled bacteria exhibit chemotaxis (chemotaxis ratio was 1.85±0.04) toward green fluorescent protein (GFP)-labeled TR4 hyphae in banana plants. We conclude that B. subtilis, B. velezensis, and B. amyloliquefaciens can successfully colonize banana plants and interact with TR4. Monitoring its dynamic interaction with TR4 and its biocontrol mechanism is under further study.
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Affiliation(s)
- Ping He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming, China.,Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Shu Li
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Shengtao Xu
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Huacai Fan
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yongfen Wang
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Institute of Tropical and Subtropical Industry Crops, Yunnan Academy of Agricultural Sciences, Baoshan, China
| | - Wei Zhou
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Gang Fu
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Guangyu Han
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Yun-Yue Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Si-Jun Zheng
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Bioversity International, Kunming, China
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10
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Ji M, Liu Y, Wu H, Li S, Duan H, Shi J, Sun J. Engineering Bacillus subtilis ATCC 6051a for the production of recombinant catalases. J Ind Microbiol Biotechnol 2021; 48:6177681. [PMID: 33734388 PMCID: PMC9113483 DOI: 10.1093/jimb/kuab024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/13/2021] [Indexed: 11/14/2022]
Abstract
Catalases are a large group of enzymes that decompose hydrogen peroxide to oxygen and hydrogen, and have been applied widely in numerous areas. Bacillus subtilis ATCC 6051a is a well-known host strain for high level secretion of heterologous peptides. However, the application of 6051a was seriously hampered by insufficient transformation efficiency. In this study, D-xylose inducible comK was integrated into the genome of B. subtilis ATCC 6051a, generating 164S, a mutant owns a transformation efficiency of 1 000-fold higher than its parent strain, thus allowing gene replacement by double crossover recombination using linear dsDNAs. The efficiency of the flanking arms for homologous recombination was then analyzed. We found that 400 bp was the minimal length of homologous fragments required to initiate efficient recombination in the 164S strain. In addition, DNA cassettes encoding two mesophilic catalases (Orf 2-62 and Orf 2-63) from B. licheniformis were integrated onto 164S. The catalytic properties of recombinant Orf 2-62 and Orf 2-63 were analyzed, and were found to be predominantly secreted into the fermentation broth, although they obviously lack any known secretory signal peptide. This work demonstrated that B. subtilis 164S is an excellent cell tool, not only for its superior secretion capacity, but also for its convenience in genetic modification.
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Affiliation(s)
- Minghua Ji
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunhui Liu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Haiying Wu
- Materials and Physical Biology Division School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Sijie Li
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China
| | - Haiyan Duan
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jiping Shi
- Correspondence should be addressed to: Jiping Shi. Phone: +86-21-20325163. E-mail:
| | - Junsong Sun
- Correspondence should be addressed to: Junsong Sun. Phone: +86-21-20325163. E-mail:
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Wang R, Liang X, Long Z, Wang X, Yang L, Lu B, Gao J. An LCI-like protein APC 2 protects ginseng root from Fusarium solani infection. J Appl Microbiol 2020; 130:165-178. [PMID: 32639629 DOI: 10.1111/jam.14771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/25/2020] [Accepted: 07/02/2020] [Indexed: 11/29/2022]
Abstract
AIMS We aimed to purify an antimicrobial protein from Bacillus amyloliquefaciens FS6 culture supernatant, verify its antimicrobial activity against Fusarium solani and evaluate its biocontrol potential for ginseng root rot. METHODS AND RESULTS The antimicrobial protein was purified from FS6 culture supernatant using ammonium sulphate precipitation, anion exchange and gel chromatography. Based on mass spectrometry results, the purified protein was identified as an antimicrobial protein of the LCI family and was designated APC2 . The APC2 recombinant protein expressed in Escherichia coli (BL21) significantly inhibited F. solani and decreased the infection and spread of F. solani in ginseng root. An overexpressing APC2 strain FS6-APC2 was constructed and shown to have enhanced antimicrobial activity compared to the wild-type strain FS6. CONCLUSIONS The APC2 protein shows strong antimicrobial activity against F. solani, reduces the incidence and severity of ginseng root rot caused by F. solani and exhibits a great biocontrol potential. SIGNIFICANCE AND IMPACT OF THE STUDY This study reports the inhibitory activity of APC2 protein (LCI family) against F. solani and its protective efficacy on ginseng root rot. These findings provide a scientific basis for future research on the biocontrol mechanism, as well as the development and application of FS6.
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Affiliation(s)
- R Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin, China
| | - X Liang
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin, China
| | - Z Long
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin, China
| | - X Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin, China
| | - L Yang
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin, China
| | - B Lu
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin, China
| | - J Gao
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin, China
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Wang A, Hua J, Wang Y, Zhang G, Luo S. Stereoisomers of Nonvolatile Acetylbutanediol Metabolites Produced by Bacillus velezensis WRN031 Improved Root Elongation of Maize and Rice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6308-6315. [PMID: 32396372 DOI: 10.1021/acs.jafc.0c01352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Inoculation of crop plants with strains of beneficial bacteria can result in promotion of plant growth. In our study, we demonstrated that Bacillus velezensis WRN031 as a plant-growth-promoting rhizobacteria (PGPR) improved the maize seedling growth following inoculation with WRN031. Fluorescence microscopy visualization indicated that GFP-labeled B. velezensis WRN031 had accumulated on the maturation zones of both primary and lateral roots of maize. Two metabolites were detected in the rhizosphere soil of maize root inoculation with WRN031 using HPLC-DAD analyses. Through guided isolation from an ethyl acetate extract of B. velezensis WRN031, these two nonvolatile meso stereoisomers 3S,4R-acetylbutanediol (3S,4R-ABD, 1) and 3R,4R-acetylbutanediol (3R,4R-ABD, 2) were identified and found to occur at a ratio of 1:2 (v/v) in maize rhizosphere soil. Bioactivity screening indicated that compounds 1 and 2, as well as a v/v = 1:2 mixture of both 1 and 2, significantly improved the root elongation of both maize and rice, with the effective enhancement concentration related to their concentration in rhizosphere soil. These results suggested that 3S,4R-ABD and 3R,4R-ABD produced by B. velezensis WRN031 might improve the growth of their host plants and provides evidence that nonvolatiles accumulating in the root maturation zone may regulate the relationship between roots and beneficial bacteria.
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Affiliation(s)
- Anqi Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, P. R. China
| | - Juan Hua
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, P. R. China
| | - Yangyang Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, P. R. China
| | - Guishan Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Shihong Luo
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, P. R. China
- Key Laboratory of Biological Invasions and Global Changes, Shenyang 110161, P. R. China
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Tang S, Xu T, Peng J, Zhou K, Zhu Y, Zhou W, Cheng H, Zhou H. Overexpression of an endogenous raw starch digesting mesophilic α-amylase gene in Bacillus amyloliquefaciens Z3 by in vitro methylation protocol. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:3013-3023. [PMID: 32056215 DOI: 10.1002/jsfa.10332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/07/2020] [Accepted: 02/13/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Mesophilic α-amylases function effectively at low temperatures with high rates of catalysis and require less energy for starch hydrolysis. Bacillus amyloliquefaciens is an essential producer of mesophilic α-amylases. However, because of the existence of the restriction-modification system, introducing exogenous DNAs into wild-type B. amyloliquefaciens is especially tricky. RESULTS α-Amylase producer B. amyloliquefaciens strain Z3 was screened and used as host for endogenous α-amylase gene expression. In vitro methylation was performed in recombinant plasmid pWB980-amyZ3. With the in vitro methylation, the transformation efficiency was increased to 0.96 × 102 colony-forming units μg-1 plasmid DNA. A positive transformant BAZ3-16 with the highest α-amylase secreting capacity was chosen for further experiments. The α-amylase activity of strain BAZ3-16 reached 288.70 ± 16.15 U mL-1 in the flask and 386.03 ± 16.25 U mL-1 in the 5-L stirred-tank fermenter, respectively. The Bacillus amyloliquefaciens Z3 expression system shows excellent genetic stability and high-level extracellular production of the target protein. Moreover, the synergistic interaction of AmyZ3 with amyloglucosidase was determined during the hydrolysis of raw starch. The hydrolysis degree reached 92.34 ± 3.41% for 100 g L-1 raw corn starch and 81.30 ± 2.92% for 100 g L-1 raw cassava starch after 24 h, respectively. CONCLUSION Methylation of the plasmid DNA removes a substantial barrier for transformation of B. amyloliquefaciens strain Z3. Furthermore, the exceptional ability to hydrolyze starch makes α-amylase AmyZ3 and strain BAZ3-16 valuable in the starch industry. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Shizhe Tang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Tingliang Xu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jing Peng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Kaiyan Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yuling Zhu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Wenbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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Yi J, Zhang D, Cheng Y, Tan J, Luo Y. The impact of Paenibacillus polymyxa HY96-2 luxS on biofilm formation and control of tomato bacterial wilt. Appl Microbiol Biotechnol 2019; 103:9643-9657. [PMID: 31686149 PMCID: PMC6867978 DOI: 10.1007/s00253-019-10162-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/27/2019] [Accepted: 09/28/2019] [Indexed: 12/24/2022]
Abstract
The focus of this study was to investigate the effects of luxS, a key regulatory gene of the autoinducer-2 (AI-2) quorum sensing (QS) system, on the biofilm formation and biocontrol efficacy against Ralstonia solanacearum by Paenibacillus polymyxa HY96-2. luxS mutants were constructed and assayed for biofilm formation of the wild-type (WT) strain and luxS mutants of P. polymyxa HY96-2 in vitro and in vivo. The results showed that luxS positively regulated the biofilm formation of HY96-2. Greenhouse experiments of tomato bacterial wilt found that from the early stage to late stage postinoculation, the biocontrol efficacy of the luxS deletion strain was the lowest with 50.70 ± 1.39% in the late stage. However, the luxS overexpression strain had the highest biocontrol efficacy with 75.66 ± 1.94% in the late stage. The complementation of luxS could restore the biocontrol efficacy of the luxS deletion strain with 69.84 ± 1.09% in the late stage, which was higher than that of the WT strain with 65.94 ± 2.73%. Therefore, we deduced that luxS could promote the biofilm formation of P. polymyxa HY96-2 and further promoted its biocontrol efficacy against R. solanacearum.
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Affiliation(s)
- Jincui Yi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Daojing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuejuan Cheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jingjing Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuanchan Luo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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Morales-Ruiz E, López-Ceballos A, Maldonado-Mendoza IE. Transformation of the rhizospheric Bacillus cereus sensu lato B25 strain using a room-temperature electrocompetent cells preparation protocol. Plasmid 2019; 105:102435. [DOI: 10.1016/j.plasmid.2019.102435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 11/26/2022]
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Gheibi A, Khanahmad H, Kardar GA, Boshtam M, Rezaie S, Kazemi B, Khorramizadeh MR. Optimization and Comparison of Different Methods and Factors for Efficient Transformation of Brucella abortus RB51strain. Adv Biomed Res 2019; 8:37. [PMID: 31198771 PMCID: PMC6555225 DOI: 10.4103/abr.abr_14_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: The development of protective vaccines for Brucella spp. has been hampered by the difficulty in transformation of Brucella cells with foreign DNA for genetic manipulation. It seems that the formation of Brucella spheroplasts would increase the efficiency of transformation. The aim of this study was to devise an efficient method for the transformation of Brucella spp. Materials and Methods: At first, spheroplast of Brucella was prepared by glycine and ampicillin induction and transformed using optimized protocols of CaCl2, electroporation, and lipofection methods. Then, the efficacy of transformation was compared between the three-mentioned methods. Results: Ampicillin-induced spheroplasts from early-log phase culture of brucella when incubated in a medium-containing 0.2 M sucrose during cell recovery had higher transformation efficiency in three different methods. Comparison of the transformation efficiency of Brucella abortus RB51 using the CaCl2, lipofection, and electroporation methods revealed that the transformation efficiency with the lipofection method was significantly higher than with other two methods (P < 0.05). Conclusions: Lipofection method by lipofectamine 2000 on ampicillin-induced spheroplasts can be a suitable approach for Brucella transformation.
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Affiliation(s)
- Azam Gheibi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Gholam Ali Kardar
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, Asthma and Allergy Research Institute, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Boshtam
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sassan Rezaie
- Department of Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Khorramizadeh
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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Biofilm Formation and Synthesis of Antimicrobial Compounds by the Biocontrol Agent Bacillus velezensis QST713 in an Agaricus bisporus Compost Micromodel. Appl Environ Microbiol 2019; 85:AEM.00327-19. [PMID: 30979839 DOI: 10.1128/aem.00327-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/07/2019] [Indexed: 12/22/2022] Open
Abstract
Bacillus velezensis QST713 is widely used as a biological control agent for crop protection and disease suppression. This strain is used industrially in France for the protection of Agaricus bisporus against Trichoderma aggressivum f. europaeum, which causes green mold disease. The efficacy of this biocontrol process was evaluated in a previous study, yet the mode of its action has not been explored under production conditions. In order to decipher the underlying biocontrol mechanisms for effective biofilm formation by strain QST713 in the compost and for the involvement of antimicrobial compounds, we developed a simplified micromodel for the culture of A. bisporus during its early culture cycle. By using this micromodel system, we studied the transcriptional response of strain QST713 in the presence or absence of A. bisporus and/or T. aggressivum in axenic industrial compost. We report the overexpression of several genes of the biocontrol agent involved in biofilm formation in the compost compared to their expression during growth in broth compost extract either in the exponential growth phase (the epsC, blsA, and tapA genes) or in the stationary growth phase (the tapA gene), while a gene encoding a flagellar protein (hag) was underexpressed. We also report the overexpression of Bacillus velezensis QST713 genes related to surfactin (srfAA) and fengycin (fenA) production in the presence of the fungal pathogen in the compost.IMPORTANCE Biocontrol agents are increasingly used to replace chemical pesticides to prevent crop diseases. In the button mushroom field in France, the use of Bacillus velezensis QST713 as a biocontrol agent against the green mold Trichoderma aggressivum has been shown to be efficient. However, the biocontrol mechanisms effective in the Agaricus bisporus/Trichoderma aggressivum/Bacillus velezensis QST713 pathosystem are still unknown. Our paper focuses on the exploration of the bioprotection mechanisms of the biocontrol agent Bacillus velezensis QST713 during culture of the button mushroom (Agaricus bisporus) in a micromodel culture system to study the specific response of strain QST713 in the presence of T. aggressivum and/or A. bisporus.
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Qiu Y, Zhu Y, Zhang Y, Sha Y, Xu Z, Li S, Feng X, Xu H. Characterization of a Regulator pgsR on Endogenous Plasmid p2Sip and Its Complementation for Poly(γ-glutamic acid) Accumulation in Bacillus amyloliquefaciens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3711-3722. [PMID: 30866628 DOI: 10.1021/acs.jafc.9b00332] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacillus amyloliquefaciens NX-2S154 is a promising poly(γ-glutamic acid) (γ-PGA) producing strain discovered in previous studies. However, the wild-type strain contains an unknown endogenous plasmid, p2Sip, which causes low transformation efficiency and instability of exogenous plasmids. In our study, p2Sip is 5622 bp with 41% G+C content and contains four putative open reading frames (ORFs), including genes repB, hsp, and mobB and γ-PGA-synthesis regulator, pgsR. Elimination of p2Sip from strain NX-2S154 delayed γ-PGA secretion and decreased production of γ-PGA by 18.1%. Integration of a pgsR expression element into the genomic BamHI locus using marker-free manipulation based on pheS* increased the γ-PGA titer by 8%. pgsR overexpression upregulated the expression of γ-PGA synthase pgsB, regulator degQ, and glutamic acid synthase gltA, thus increasing the γ-PGA production in B. amyloliquefaciens NB. Our results indicated that pgsR from p2Sip plays an important regulatory role in γ-PGA synthesis in B. amyloliquefaciens.
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Affiliation(s)
- Yibin Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
| | - Yifan Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
| | - Yatao Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
| | - Yuanyuan Sha
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
| | - Zongqi Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
| | - Xiaohai Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing 211816 , China
- College of Food Science and Light Industry , Nanjing Tech University , Nanjing 211816 , China
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Zhou C, Liu H, Yuan F, Chai H, Wang H, Liu F, Li Y, Zhang H, Lu F. Development and application of a CRISPR/Cas9 system for Bacillus licheniformis genome editing. Int J Biol Macromol 2019; 122:329-337. [PMID: 30401651 DOI: 10.1016/j.ijbiomac.2018.10.170] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 10/28/2022]
Abstract
A highly efficient genome editing system for Bacillus licheniformis was developed based on single-plasmid CRISPR/Cas9. For highly efficient genome editing the shuttle vector pWH1520 was selected to construct the knockout plasmids. A construct harboring a pS promoter driving cas9 endonuclease expression, a strong pLY-2 promoter driving the transcription of a single guide RNA was demonstrated as being the most effective. To verify the feasibility of the method the uprT gene coding uracil phosphoribosyltransferase was selected as the reporter gene. The efficiency of introducing nucleotide point mutations and single gene deletion reached an editing efficiency of up to 99.2% and 97.3%, respectively. After a upp-deficient strain was engineered, the system and strain were applied to introduce genomic deletions of another two genes, amyL and chiA (encoding amylase and chitinase, respectively) with about 90% deletion efficiency. As two native extracellular proteins with relatively high secretion in the host, amylase and chitinase can hamper the secretion and expression of alkaline protease. It was demonstrated that the mutant with deletions of the two genes effectively improved the alkaline protease yield by 24.8%. The results illustrated that the establishment of a CRISPR/Cas9 system for Bacillus licheniformis is of significance, and confirmed the system's high efficiency. The system provides support for effective molecular modification and metabolic regulation of Bacillus licheniformis, and offers promise for applications in genetic modification of other industrially relevant Bacillus species.
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Affiliation(s)
- Cuixia Zhou
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China
| | - Huan Liu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China
| | - Feiyan Yuan
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China
| | - Haonan Chai
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China
| | - Haikuan Wang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China
| | - Fufeng Liu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China
| | - Yu Li
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China
| | - Huitu Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China.
| | - Fuping Lu
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 022, PR China.
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Development of Bacillus amyloliquefaciens as a high-level recombinant protein expression system. ACTA ACUST UNITED AC 2019; 46:113-123. [DOI: 10.1007/s10295-018-2089-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 10/15/2018] [Indexed: 12/29/2022]
Abstract
Abstract
Bacillus amyloliquefaciens K11 is a hyperproducer of extracellular neutral protease, which can produce recombinant homologous protein steadily and is amenable to scale up to high-cell density fermentation. The present study aims to genetically modify strain K11 as a highly efficient secretory expression system for high-level production of heterologous proteins. Using B. amyloliquefaciens K11 and alkaline protease gene BcaprE as the expression host and model gene, the gene expression levels mediated by combinations of promoters PamyQ, PaprE and Pnpr and signal peptides SPamyQ, SPaprE and SPnpr were assessed on shake flask level. The PamyQ-SPaprE was found to be the best secretory expression cassette, giving the highest enzyme activities of extracellular BcaprE (13,800 ± 308 U/mL). Using the same expression system, the maltogenic α-amylase Gs-MAase and neutral protease BaNPR were successfully produced with the enzyme activities of 19. ± 0.2 U/mL and 17,495 ± 417 U/mL, respectively. After knocking out the endogenous neutral protease-encoding gene Banpr, the enzyme activities of BcaprE and Gs-MAase were further improved by 25.4% and 19.4%, respectively. Moreover, the enzyme activities of BcaprE were further improved to 30,200 ± 312 U/mL in a 15 L fermenter following optimization of the fermentation conditions. In the present study, the genetically engineered B. amyloliquefaciens strain 7-6 containing PamyQ-SPaprE as the secretory expression cassette was developed. This efficient expression system shows general applicability and represents an excellent industrial strain for the production of heterologous proteins.
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Al-Ali A, Deravel J, Krier F, Béchet M, Ongena M, Jacques P. Biofilm formation is determinant in tomato rhizosphere colonization by Bacillus velezensis FZB42. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:29910-29920. [PMID: 29063401 DOI: 10.1007/s11356-017-0469-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 10/10/2017] [Indexed: 06/07/2023]
Abstract
In this work, the behavior in tomato rhizosphere of Bacillus velezensis FZB42 was analyzed taking into account the surfactin production, the use of tomato roots exudate as substrates, and the biofilm formation. B. velezensis FZB42 and B. amyloliquefaciens S499 have a similar capability to colonize tomato rhizosphere. Little difference in this colonization was observed with surfactin non producing B. velezensis FZB42 mutant strains. B. velezensis is able to grow in the presence of root exudate and used preferentially sucrose, maltose, glutamic, and malic acids as carbon sources. A mutant enable to produce exopolysaccharide (EPS-) was constructed to demonstrate the main importance of biofilm formation on rhizosphere colonization. This mutant had completely lost its ability to form biofilm whatever the substrate present in the culture medium and was unable to efficiently colonize tomato rhizosphere.
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Affiliation(s)
- Ameen Al-Ali
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France
- College of Agriculture-Soil, Water and Environmental Research Department, Al-Qasim Green University, Babylon, Iraq
| | - Jovana Deravel
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France
| | - François Krier
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France.
| | - Max Béchet
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France
| | - Marc Ongena
- Terra Teaching and Research Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liege, B 5030, Gembloux, Belgium
| | - Philippe Jacques
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France
- Terra Teaching and Research Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liege, B 5030, Gembloux, Belgium
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Kang JE, Kim HD, Park SY, Pan JG, Kim JH, Yum DY. Dietary Supplementation With a Bacillus Superoxide Dismutase Protects Against γ-Radiation-induced Oxidative Stress and Ameliorates Dextran Sulphate Sodium-induced Ulcerative Colitis in Mice. J Crohns Colitis 2018; 12:860-869. [PMID: 29547907 DOI: 10.1093/ecco-jcc/jjy034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/13/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Commercial superoxide dismutase [SOD] is derived from melon extract and has a potential as a dietary supplement due to its beneficial antioxidative effects. We aimed to improve the productivity of SOD compared with plant SOD by using a generally regarded as safe [GRAS] microorganism, Bacillus amyloliquefaciens, and assess its antioxidative effect using γ-radiation- and dextransulphate sodium [DSS]-induced oxidative models in mice. METHODS We identified the sodA gene encoding manganese-containing SODs [Mn-SOD] in B. amyloliquefaciens, constructed a Mn-SOD deficient mutant, and screened a high-SOD-producing strain. We compared the antioxidative effect of orally administered enteric-coated SOD protein partially purified from B. amyloliquefaciens with wild-type and high-SOD-producing strain spores. The effect of SOD on DSS-induced colitis was also investigated. Colonic inflammation was assessed using disease activity index, macroscopic and histological damage scores, antioxidant enzyme activities, and inflammatory cytokines. RESULTS The SOD activity of B. amyloliquefaciens is derived from secreted Mn-SOD encoded by the sodA gene, as shown by comparing sodA knock-out mutant spores with wild-type and high-SOD-producing spores. Enteric-coated SOD of B. amyloliquefaciens appears to be effective in reducing oxidative stress in γ-radiation- and DSS-induced mouse models. Co-administration of SOD with wild-type B. amyloliquefaciens or high-SOD-producer strain spores showed a synergistic effect. SOD enzyme and B. amyloliquefaciens spores contribute to the reduction of oxidative stress and inflammatory response in DSS-induced colitis. CONCLUSIONS Mn-SOD of B. amyloliquefaciens could be another source of SOD supplement and may be useful to prevent and treat ulcerative colitis.
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Affiliation(s)
- Ji-Eun Kang
- GenoFocus, Inc., Techno 1-ro, Yuseong-gu, Daejeon, Korea
| | - Hyun-Do Kim
- GenoFocus, Inc., Techno 1-ro, Yuseong-gu, Daejeon, Korea
| | - Soo-Young Park
- GenoFocus, Inc., Techno 1-ro, Yuseong-gu, Daejeon, Korea
| | - Jae-Gu Pan
- GenoFocus, Inc., Techno 1-ro, Yuseong-gu, Daejeon, Korea
| | - Jeong Hyun Kim
- GenoFocus, Inc., Techno 1-ro, Yuseong-gu, Daejeon, Korea
| | - Do-Young Yum
- GenoFocus, Inc., Techno 1-ro, Yuseong-gu, Daejeon, Korea
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23
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Chang JJ, Anandharaj M, Ho CY, Tsuge K, Tsai TY, Ke HM, Lin YJ, Ha Tran MD, Li WH, Huang CC. Biomimetic strategy for constructing Clostridium thermocellum cellulosomal operons in Bacillus subtilis. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:157. [PMID: 29930703 PMCID: PMC5991470 DOI: 10.1186/s13068-018-1151-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Enzymatic conversion of lignocellulosic biomass into soluble sugars is a major bottleneck in the plant biomass utilization. Several anaerobic organisms cope these issues via multiple-enzyme complex system so called 'cellulosome'. Hence, we proposed a "biomimic operon" concept for making an artificial cellulosome which can be used as a promising tool for the expression of cellulosomal enzymes in Bacillus subtilis. RESULTS According to the proteomic analysis of Clostridium thermocellum ATCC27405 induced by Avicel or cellobiose, we selected eight highly expressed cellulosomal genes including a scaffoldin protein gene (cipA), a cell-surface anchor gene (sdbA), two exoglucanase genes (celK and celS), two endoglucanase genes (celA and celR), and two xylanase genes (xynC and xynZ). Arranging these eight genes in two different orders, we constructed two different polycistronic operons using the ordered gene assembly in Bacillus method. This is the first study to express the whole CipA along with cellulolytic enzymes in B. subtilis. Each operon was successfully expressed in B. subtilis RM125, and the protein complex assembly, cellulose-binding ability, thermostability, and cellulolytic activity were demonstrated. The operon with a higher xylanase activity showed greater saccharification on complex cellulosic substrates such as Napier grass than the other operon. CONCLUSIONS In this study, a strategy for constructing an efficient cellulosome system was developed and two different artificial cellulosomal operons were constructed. Both operons could efficiently express the cellulosomal enzymes and exhibited cellulose saccharification. This strategy can be applied to different industries with cellulose-containing materials, such as papermaking, biofuel, agricultural compost, mushroom cultivation, and waste processing industries.
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Affiliation(s)
- Jui-Jen Chang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, 402 Taiwan
| | - Marimuthu Anandharaj
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529 Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Cheng-Yu Ho
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Kenji Tsuge
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihoji, Tsuruoka, Yamagata 997-0017 Japan
| | - Tsung-Yu Tsai
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Yu-Ju Lin
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Minh Dung Ha Tran
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529 Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227 Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529 Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227 Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, 40227 Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227 Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, 40227 Taiwan
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24
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Yang Y, Li Y, Gao T, Zhang Y, Wang Q. C-di-GMP turnover influences motility and biofilm formation in Bacillus amyloliquefaciens PG12. Res Microbiol 2018; 169:205-213. [PMID: 29859892 DOI: 10.1016/j.resmic.2018.04.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 03/22/2018] [Accepted: 04/05/2018] [Indexed: 12/11/2022]
Abstract
Bis-(3'→5') cyclic dimeric guanosine monophosphate (c-di-GMP) is defined as a highly versatile secondary messenger in bacteria, coordinating diverse aspects of bacterial growth and behavior, including motility and biofilm formation. Bacillus amyloliquefaciens PG12 is an effective biocontrol agent against apple ring rot caused by Botryosphaeria dothidea. In this study, we characterized the core regulators of c-di-GMP turnover in B. amyloliquefaciens PG12. Using bioinformatic analysis, heterologous expression and biochemical characterization of knockout and overexpression derivatives, we identified and characterized two active diguanylate cyclases (which catalyze c-di-GMP biosynthesis), YhcK and YtrP and one active c-di-GMP phosphodiesterase (which degrades c-di-GMP), YuxH. Furthermore, we showed that elevating c-di-GMP levels up to a certain threshold inhibited the swimming motility of B. amyloliquefaciens PG12. Although yhcK, ytrP and yuxH knockout mutants did not display defects in biofilm formation, significant increases in c-di-GMP levels induced by YtrP or YuxH overexpression stimulated biofilm formation in B. amyloliquefaciens PG12. Our results indicate that B. amyloliquefaciens possesses a functional c-di-GMP signaling system that influences the bacterium's motility and ability to form biofilms. Since motility and biofilm formation influence the efficacy of biological control agent, our work provides a basis for engineering a more effective strain of B. amyloliquefaciens PG12.
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Affiliation(s)
- Yang Yang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Yan Li
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Tantan Gao
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Yue Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Qi Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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25
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Wu J, Deng A, Sun Q, Bai H, Sun Z, Shang X, Zhang Y, Liu Q, Liang Y, Liu S, Che Y, Wen T. Bacterial Genome Editing via a Designed Toxin-Antitoxin Cassette. ACS Synth Biol 2018; 7:822-831. [PMID: 28094982 DOI: 10.1021/acssynbio.6b00287] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Manipulating the bacterial genomes in an efficient manner is essential to biological and biotechnological research. Here, we reprogrammed the bacterial TA systems as the toxin counter-selectable cassette regulated by an antitoxin switch (TCCRAS) for genetic modifications in the extensively studied and utilized Gram-positive bacteria, B. subtilis and Corynebacterium glutamicum. In the five characterized type II TA systems, the RelBE complex can specifically and efficiently regulate cell growth and death by the conditionally controlled antitoxin RelB switch, thereby serving as a novel counter-selectable cassette to establish the TCCRAS system. Using a single vector, such a system has been employed to perform in-frame deletion, functional knock-in, gene replacement, precise point mutation, large-scale insertion, and especially, deletion of the fragments up to 194.9 kb in B. subtilis. In addition, the biosynthesis of lycopene was first achieved in B. subtilis using TCCRAS to integrate a 5.4-kb fusion cluster ( P spac- crtI- crtE- crtB). The system was further adapted for gene knockdown and replacement, and large-scale deletion of the fragments up to 179.8 kb in C. glutamicum, with the mutation efficiencies increased by 0.8-1.0-fold compared to the conventional SacB method. TCCRAS thus holds promise as an effective and versatile genome-scale engineering technology for metabolic engineering and synthetic genomics research in a broad range of the Gram-positive bacteria.
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Affiliation(s)
- Jie Wu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Aihua Deng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinyun Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Bai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaopeng Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiuling Shang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong Liang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuwen Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongsheng Che
- State Key Laboratory of Toxicology & Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid medical school, University of Chinese Academy of Sciences, Beijing 100049, China
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26
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Tee KL, Grinham J, Othusitse AM, González-Villanueva M, Johnson AO, Wong TS. An Efficient Transformation Method for the Bioplastic-Producing “Knallgas” Bacterium Ralstonia eutropha
H16. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700081] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 07/14/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Kang Lan Tee
- Department of Chemical and Biological Engineering, ChELSI Institute and Advanced Biomanufacturing Centre; The University of Sheffield; Sheffield United Kingdom
| | - James Grinham
- Department of Chemical and Biological Engineering, ChELSI Institute and Advanced Biomanufacturing Centre; The University of Sheffield; Sheffield United Kingdom
| | - Arona M. Othusitse
- Department of Chemical and Biological Engineering, ChELSI Institute and Advanced Biomanufacturing Centre; The University of Sheffield; Sheffield United Kingdom
| | - Miriam González-Villanueva
- Department of Chemical and Biological Engineering, ChELSI Institute and Advanced Biomanufacturing Centre; The University of Sheffield; Sheffield United Kingdom
| | - Abayomi O. Johnson
- Department of Chemical and Biological Engineering, ChELSI Institute and Advanced Biomanufacturing Centre; The University of Sheffield; Sheffield United Kingdom
| | - Tuck Seng Wong
- Department of Chemical and Biological Engineering, ChELSI Institute and Advanced Biomanufacturing Centre; The University of Sheffield; Sheffield United Kingdom
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27
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Development of an efficient electroporation method for rhizobacterial Bacillus mycoides strains. J Microbiol Methods 2017; 133:82-86. [DOI: 10.1016/j.mimet.2016.12.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 12/23/2016] [Accepted: 12/23/2016] [Indexed: 11/22/2022]
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28
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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: 0.3] [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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29
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Zhou C, Shi L, Ye B, Feng H, Zhang J, Zhang R, Yan X. pheS * , an effective host-genotype-independent counter-selectable marker for marker-free chromosome deletion in Bacillus amyloliquefaciens. Appl Microbiol Biotechnol 2016; 101:217-227. [PMID: 27730334 DOI: 10.1007/s00253-016-7906-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/15/2016] [Accepted: 09/25/2016] [Indexed: 12/22/2022]
Abstract
Aside from applications in the production of commercial enzymes and metabolites, Bacillus amyloliquefaciens is also an important group of plant growth-promoting rhizobacteria that supports plant growth and suppresses phytopathogens. A host-genotype-independent counter-selectable marker would enable rapid genetic manipulation and metabolic engineering, accelerating the study of B. amyloliquefaciens and its development as both a microbial cell factory and plant growth-promoting rhizobacteria. Here, a host-genotype-independent counter-selectable marker pheS * was constructed through a point mutation of the gene pheS, which encodes the α-subunit of phenylalanyl-tRNA synthetase in Bacillus subtilis strain 168. In the presence of 5 mM p-chloro-phenylalanine, 100 % of B. amyloliquefaciens strain SQR9 cells carrying pheS * were killed, whereas the wild-type strain SQR9 showed resistance to p-chloro-phenylalanine. A simple pheS * and overlap-PCR-based strategy was developed to create the marker-free deletion of the amyE gene as well as a 37-kb bmy cluster in B. amyloliquefaciens SQR9. The effectiveness of pheS * as a counter-selectable marker in B. amyloliquefaciens was further confirmed through the deletion of amyE genes in strains B. amyloliquefaciens FZB42 and NJN-6. In addition, the potential use of pheS * in other Bacillus species was preliminarily assessed. The expression of PheS* in B. subtilis strain 168 and B. cereus strain ATCC 14579 caused pronounced sensitivity of both hosts to p-chloro-phenylalanine, indicating that pheS * could be used as a counter-selectable marker (CSM) in these strains.
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Affiliation(s)
- Chaoyang Zhou
- Department of Microbiology, College of Life Sciences, Key Laboratory for Microbiological Engineering of Agricultural, Environment of Ministry of Agriculture, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Lingling Shi
- Department of Microbiology, College of Life Sciences, Key Laboratory for Microbiological Engineering of Agricultural, Environment of Ministry of Agriculture, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Bin Ye
- Department of Microbiology, College of Life Sciences, Key Laboratory for Microbiological Engineering of Agricultural, Environment of Ministry of Agriculture, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Haichao Feng
- National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Ji Zhang
- Jiangsu Key Laboratory for Chemistry of Low-Dimensional Materials, School of Chemistry and Chemical Engineering, Huaiyin Normal University, Huaian, 223300, People's Republic of China
| | - Ruifu Zhang
- National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Xin Yan
- Department of Microbiology, College of Life Sciences, Key Laboratory for Microbiological Engineering of Agricultural, Environment of Ministry of Agriculture, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China.
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A new strategy to express the extracellular α-amylase from Pyrococcus furiosus in Bacillus amyloliquefaciens. Sci Rep 2016; 6:22229. [PMID: 26916714 PMCID: PMC4768087 DOI: 10.1038/srep22229] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/05/2016] [Indexed: 11/12/2022] Open
Abstract
Extracellular α-amylase from Pyrococcus furiosus (PFA) shows great starch-processing potential for industrial application due to its thermostability, long half-life and optimal activity at low pH; however, it is difficult to produce in large quantities. In contrast, α-amylase from Bacillus amyloliquefaciens (BAA) can be produced in larger quantities, but shows lower stability at high temperatures and low pH. Here, we describe a BAA protein expression pattern-mimicking strategy to express PFA in B. amyloliquefaciens using the expression and secretion elements of BAA, including the codon usage bias and mRNA structure of gene, promoter, signal peptide, host and cultivation conditions. This design was assessed to be successful by comparing the various genes (mpfa and opfa), promoters (PamyA and P43), and strains (F30, F31, F32 and F30-∆amyA). The final production of PFA yielded 2714 U/mL, about 3000- and 14-fold that reportedly produced in B. subtilis or E. coli, respectively. The recombinant PFA was optimally active at ~100 °C and pH 5 and did not require Ca2+ for activity or thermostability, and >80% of the enzyme activity was retained after treatment at 100 °C for 4 h.
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31
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Wang H, Yang L, Ping Y, Bai Y, Luo H, Huang H, Yao B. Engineering of a Bacillus amyloliquefaciens Strain with High Neutral Protease Producing Capacity and Optimization of Its Fermentation Conditions. PLoS One 2016; 11:e0146373. [PMID: 26752595 PMCID: PMC4708984 DOI: 10.1371/journal.pone.0146373] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 12/16/2015] [Indexed: 01/03/2023] Open
Abstract
The neutral protease has high potential for industrial applications, and attempts to improve enzyme expression level have important application values. In the present study, a neutral protease-encoding gene, Banpr, was cloned from Bacillus amyloliquefaciens strain K11, and a genetic manipulation method specific for this difficult-to-transform strain was developed for the high-level expression of neutral protease. The recombinant plasmid pUB110-Banpr was constructed in Bacillus subtilis strain WB600 and then transformed into strain K11 under optimized conditions. A positive transformant 110N-6 with the highest protease secreting capacity on skim milk plates and great genetic stability for more than 100 generations was selected for further study. Optimization of the fermentation conditions increased the enzyme activity of strain 110N-6 to 8995 ± 250 U/ml in flask culture and 28084 ± 1282 U/ml in 15-l fermentor, which are significantly higher than that of the native strain K11 and industrial strain B. subtilis AS.1398, respectively. The high expression level and extreme genetic stability make B. amyloliquefaciens strain 110N-6 more favorable for mass production of neutral protease for industrial uses.
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Affiliation(s)
- Hui Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Lian Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yanhai Ping
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
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32
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Ruan Y, Zhu L, Li Q. Improving the electro-transformation efficiency of Corynebacterium glutamicum by weakening its cell wall and increasing the cytoplasmic membrane fluidity. Biotechnol Lett 2015; 37:2445-52. [DOI: 10.1007/s10529-015-1934-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/04/2015] [Indexed: 10/23/2022]
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33
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Development of an efficient electroporation method for iturin A-producing Bacillus subtilis ZK. Int J Mol Sci 2015; 16:7334-51. [PMID: 25837631 PMCID: PMC4425020 DOI: 10.3390/ijms16047334] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/09/2015] [Accepted: 02/11/2015] [Indexed: 01/05/2023] Open
Abstract
In order to efficiently introduce DNA into B. subtilis ZK, which produces iturin A at a high level, we optimized seven electroporation conditions and explored an efficient electroporation method. Using the optimal conditions, the electroporation efficiency was improved to 1.03 × 107 transformants/μg of DNA, an approximately 10,000-fold increase in electroporation efficiency. This efficiency is the highest electroporation efficiency for B. subtilis and enables the construction of a directed evolution library or the knockout of a gene in B. subtilis ZK for molecular genetics studies. In the optimization process, the combined effects of three types of wall-weakening agents were evaluated using a response surface methodology (RSM) design, which led to a two orders of magnitude increase in electroporation efficiency. To the best of our limited knowledge, this study provides the first demonstration of using an RSM design for optimization of the electroporation conditions for B. subtilis. To validate the electroporation efficiency, a case study was performed and a gene (rapC) was inactivated in B. subtilis ZK using a suicide plasmid pMUTIN4. Moreover, we found that the rapC mutants exhibited a marked decrease in iturin A production, suggesting that the rapC gene was closely related to the iturin A production.
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A high-efficiency recombineering system with PCR-based ssDNA in Bacillus subtilis mediated by the native phage recombinase GP35. Appl Microbiol Biotechnol 2015; 99:5151-62. [PMID: 25750031 DOI: 10.1007/s00253-015-6485-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 02/02/2015] [Accepted: 02/14/2015] [Indexed: 02/02/2023]
Abstract
Bacillus subtilis and its closely related species are important strains for industry, agriculture, and medicine. However, it is difficult to perform genetic manipulations using the endogenous recombination machinery. In many bacteria, phage recombineering systems have been employed to improve recombineering frequencies. To date, an efficient phage recombineering system for B. subtilis has not been reported. Here, we, for the first time, identified that GP35 from the native phage SPP1 exhibited a high recombination activity in B. subtilis. On this basis, we developed a high-efficiency GP35-meditated recombineering system. Taking single-stranded DNA (ssDNA) as a recombineering substrate, ten recombinases from diverse sources were investigated in B. subtilis W168. GP35 showed the highest recombineering frequency (1.71 ± 0.15 × 10(-1)). Besides targeting the purine nucleoside phosphorylase gene (deoD), we also demonstrated the utility of GP35 and Beta from Escherichia coli lambda phage by deleting the alpha-amylase gene (amyE) and uracil phosphoribosyltransferase gene (upp). In all three genetic loci, GP35 exhibited a higher frequency than Beta. Moreover, a phylogenetic tree comparing the kinship of different recombinase hosts with B. subtilis was constructed, and the relationship between the recombineering frequency and the kinship of the host was further analyzed. The results suggested that closer kinship to B. subtilis resulted in higher frequency in B. subtilis. In conclusion, the recombinase from native phage or prophage can significantly promote the genetic recombineering frequency in its host, providing an effective genetic tool for constructing genetically engineered strains and investigating bacterial physiology.
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Hossain MJ, Ran C, Liu K, Ryu CM, Rasmussen-Ivey CR, Williams MA, Hassan MK, Choi SK, Jeong H, Newman M, Kloepper JW, Liles MR. Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum. FRONTIERS IN PLANT SCIENCE 2015; 6:631. [PMID: 26347755 PMCID: PMC4538294 DOI: 10.3389/fpls.2015.00631] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 07/30/2015] [Indexed: 05/03/2023]
Abstract
To understand the growth-promoting and disease-inhibiting activities of plant growth-promoting rhizobacteria (PGPR) strains, the genomes of 12 Bacillus subtilis group strains with PGPR activity were sequenced and analyzed. These B. subtilis strains exhibited high genomic diversity, whereas the genomes of B. amyloliquefaciens strains (a member of the B. subtilis group) are highly conserved. A pairwise BLASTp matrix revealed that gene family similarity among Bacillus genomes ranges from 32 to 90%, with 2839 genes within the core genome of B. amyloliquefaciens subsp. plantarum. Comparative genomic analyses of B. amyloliquefaciens strains identified genes that are linked with biological control and colonization of roots and/or leaves, including 73 genes uniquely associated with subsp. plantarum strains that have predicted functions related to signaling, transportation, secondary metabolite production, and carbon source utilization. Although B. amyloliquefaciens subsp. plantarum strains contain gene clusters that encode many different secondary metabolites, only polyketide biosynthetic clusters that encode difficidin and macrolactin are conserved within this subspecies. To evaluate their role in plant pathogen biocontrol, genes involved in secondary metabolite biosynthesis were deleted in a B. amyloliquefaciens subsp. plantarum strain, revealing that difficidin expression is critical in reducing the severity of disease, caused by Xanthomonas axonopodis pv. vesicatoria in tomato plants. This study defines genomic features of PGPR strains and links them with biocontrol activity and with host colonization.
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Affiliation(s)
| | - Chao Ran
- Department of Biological Sciences, Auburn UniversityAuburn, AL, USA
| | - Ke Liu
- Department of Entomology and Plant Pathology, Auburn UniversityAuburn, AL, USA
| | - Choong-Min Ryu
- Superbacteria Research Center, Korea Research Institute of Bioscience & BiotechnologyDaejeon, South Korea
| | | | | | - Mohammad K. Hassan
- Department of Entomology and Plant Pathology, Auburn UniversityAuburn, AL, USA
| | - Soo-Keun Choi
- Superbacteria Research Center, Korea Research Institute of Bioscience & BiotechnologyDaejeon, South Korea
| | - Haeyoung Jeong
- Superbacteria Research Center, Korea Research Institute of Bioscience & BiotechnologyDaejeon, South Korea
| | - Molli Newman
- Department of Entomology and Plant Pathology, Auburn UniversityAuburn, AL, USA
| | - Joseph W. Kloepper
- Department of Entomology and Plant Pathology, Auburn UniversityAuburn, AL, USA
| | - Mark R. Liles
- Department of Biological Sciences, Auburn UniversityAuburn, AL, USA
- *Correspondence: Mark R. Liles, Department of Biological Sciences, Auburn University, Room 101, Rouse Life Sciences Building, 120 West Samford Avenue, Auburn, AL 36849, USA
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Lu S, Nie Y, Tang YQ, Xiong G, Wu XL. A critical combination of operating parameters can significantly increase the electrotransformation efficiency of a gram-positive Dietzia strain. J Microbiol Methods 2014; 103:144-51. [DOI: 10.1016/j.mimet.2014.05.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 12/21/2022]
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A markerless gene replacement method for B. amyloliquefaciens LL3 and its use in genome reduction and improvement of poly-γ-glutamic acid production. Appl Microbiol Biotechnol 2014; 98:8963-73. [DOI: 10.1007/s00253-014-5824-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 04/20/2014] [Accepted: 05/10/2014] [Indexed: 10/25/2022]
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Pyne ME, Bruder M, Moo-Young M, Chung DA, Chou CP. Technical guide for genetic advancement of underdeveloped and intractable Clostridium. Biotechnol Adv 2014; 32:623-41. [DOI: 10.1016/j.biotechadv.2014.04.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/10/2014] [Accepted: 04/15/2014] [Indexed: 02/04/2023]
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Establishment of an efficient transformation protocol and its application in marine-derived Bacillus strain. SCIENCE CHINA-LIFE SCIENCES 2014; 57:627-35. [PMID: 24771061 DOI: 10.1007/s11427-014-4632-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/07/2013] [Indexed: 12/31/2022]
Abstract
Marine-derived Bacillus strains have been proved to be a very promising source for natural product leads. However, transformation of environmental strains is much more difficult than that of domesticated strains. Here, we report the development of an efficient and robust electroporation-based transformation system for marine-derived Bacillus marinus B-9987, which is a macrolactin antibiotics producer and a very promising biological control agent against fungal plant diseases. The transformation efficiency was greatly enhanced 10(3)-fold by using unmethylated plasmid to bypass modification-restriction barrier, and using glycine betaine to protect cells from electrical damages during electroporation. Addition of HEPES and 2 mmol L(-1) MgCl2 further improved the efficiency by additional 2-fold, with a maximum value of 7.1×10(4) cfu/μg pHT3101. To demonstrate the feasibility and efficiency of the protocol, a green fluorescent protein reporter system was constructed; furthermore, phosphopantetheinyl transferase gene sfp, which is essential to the biosynthesis of polyketides and nonribosomal peptides, was overexpressed in B-9987, leading to increased production of macrolactin A by about 1.6-fold. In addition, this protocol is also applicable to marine-derived Bacillus licheniforms EI-34-6, indicating it could be a reference for other undomesticated Bacillus strains. To our knowledge, this is the first report regarding the transformation of marine-derived Bacillus strain.
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Zhang W, Xie H, He Y, Feng J, Gao W, Gu Y, Wang S, Song C. Chromosome integration of theVitreoscillahemoglobin gene (vgb) mediated by temperature-sensitive plasmid enhances γ-PGA production inBacillus amyloliquefaciens. FEMS Microbiol Lett 2013; 343:127-34. [DOI: 10.1111/1574-6968.12139] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 02/26/2013] [Accepted: 03/20/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Wei Zhang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education; College of Life Sciences; Nankai University; Tianjin; China
| | - Hui Xie
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education; College of Life Sciences; Nankai University; Tianjin; China
| | - Yulian He
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education; College of Life Sciences; Nankai University; Tianjin; China
| | - Jun Feng
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education; College of Life Sciences; Nankai University; Tianjin; China
| | - Weixia Gao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education; College of Life Sciences; Nankai University; Tianjin; China
| | - Yanyan Gu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education; College of Life Sciences; Nankai University; Tianjin; China
| | - Shufang Wang
- Key Laboratory of Bioactive Materials for Ministry of Education; Nankai University; Tianjin; China
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Ji J, Hu SL, Cui ZW, Li WF. Probiotic Bacillus amyloliquefaciens mediate M1 macrophage polarization in mouse bone marrow-derived macrophages. Arch Microbiol 2013; 195:349-56. [PMID: 23455449 DOI: 10.1007/s00203-013-0877-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 01/28/2013] [Accepted: 02/07/2013] [Indexed: 11/28/2022]
Abstract
Depending on the microenvironment, macrophages can acquire distinct functional phenotypes, referred to as classically activated M1 and M2. M1 macrophages are considered potent effector cells that kill intracellular pathogens, and M2 macrophages promote the resolution of wound healing. In this study, we are interested to know whether probiotic Bacillus amyloliquefaciens (Ba) can induce macrophages polarization. Real-time fluorescence PCR analysis demonstrated that the expression of IL-1β, iNOS, TNF-α and IL-6 genes for M1 macrophages was significantly increased at 1.5 h after probiotic Ba treatment compared to the probiotic Ba-free treatment (P < 0.01), whereas the expression of M2 macrophage marker genes (Arg1, Fizz1, MR, Ym1) was decreased (P < 0.05). Furthermore, the phagocytic activity was dramatically increased in the Ba-treated BMDMs using a FITC-dextran endocytosis assay. Together, these findings indicated that probiotic Ba facilitated polarization of M1 macrophages and enhanced its phagocytic capacity. The results expanded our knowledge about probiotic function-involved macrophage polarization.
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Affiliation(s)
- Jian Ji
- Key Laboratory of Animal Molecular Nutrition of Education of Ministry, College of Animal Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
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Development of a high-efficient transformation system of Bacillus pumilus strain DX01 to facilitate gene isolation via gfp-tagged insertional mutagenesis and visualize bacterial colonization of rice roots. Folia Microbiol (Praha) 2013; 58:409-17. [DOI: 10.1007/s12223-013-0223-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 01/09/2013] [Indexed: 01/21/2023]
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Zhang G, Wang W, Deng A, Sun Z, Zhang Y, Liang Y, Che Y, Wen T. A mimicking-of-DNA-methylation-patterns pipeline for overcoming the restriction barrier of bacteria. PLoS Genet 2012; 8:e1002987. [PMID: 23028379 PMCID: PMC3459991 DOI: 10.1371/journal.pgen.1002987] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 08/10/2012] [Indexed: 12/20/2022] Open
Abstract
Genetic transformation of bacteria harboring multiple Restriction-Modification (R-M) systems is often difficult using conventional methods. Here, we describe a mimicking-of-DNA-methylation-patterns (MoDMP) pipeline to address this problem in three difficult-to-transform bacterial strains. Twenty-four putative DNA methyltransferases (MTases) from these difficult-to-transform strains were cloned and expressed in an Escherichia coli strain lacking all of the known R-M systems and orphan MTases. Thirteen of these MTases exhibited DNA modification activity in Southwestern dot blot or Liquid Chromatography–Mass Spectrometry (LC–MS) assays. The active MTase genes were assembled into three operons using the Saccharomyces cerevisiae DNA assembler and were co-expressed in the E. coli strain lacking known R-M systems and orphan MTases. Thereafter, results from the dot blot and restriction enzyme digestion assays indicated that the DNA methylation patterns of the difficult-to-transform strains are mimicked in these E. coli hosts. The transformation of the Gram-positive Bacillus amyloliquefaciens TA208 and B. cereus ATCC 10987 strains with the shuttle plasmids prepared from MoDMP hosts showed increased efficiencies (up to four orders of magnitude) compared to those using the plasmids prepared from the E. coli strain lacking known R-M systems and orphan MTases or its parental strain. Additionally, the gene coding for uracil phosphoribosyltransferase (upp) was directly inactivated using non-replicative plasmids prepared from the MoDMP host in B. amyloliquefaciens TA208. Moreover, the Gram-negative chemoautotrophic Nitrobacter hamburgensis strain X14 was transformed and expressed Green Fluorescent Protein (GFP). Finally, the sequence specificities of active MTases were identified by restriction enzyme digestion, making the MoDMP system potentially useful for other strains. The effectiveness of the MoDMP pipeline in different bacterial groups suggests a universal potential. This pipeline could facilitate the functional genomics of the strains that are difficult to transform. Approximately 95% of the genome-sequenced bacteria harbor Restriction-Modification (R-M) systems. R-M systems usually occur in pairs, i.e., DNA methyltransferases (MTases) and restriction endonucleases (REases). REases can degrade invading DNA to protect the cell from infection by phages. This protecting machinery has also become the barrier for experimental genetic manipulation, because the newly introduced DNA would be degraded by the REases of the transformed bacteria. In this study we have developed a pipeline to protect DNA by methylation from cleavage by host REases. Multiple DNA MTases were cloned from three difficult-to-transform bacterial strains and co-expressed in an E. coli strain lacking all of the known endogenous R-M systems and orphan MTases. Thus, the DNA methylation patterns of these strains have become similar to that of the difficult-to-transform strains. Ultimately, the DNA prepared from these E. coli strains can overcome the R-M barrier of the bacterial strains that are difficult to transform and achieve genetic manipulation. The effectiveness of this pipeline in different bacterial groups suggests a universal potential. This pipeline could facilitate functional genomics of bacterial strains that are difficult to transform.
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Affiliation(s)
- Guoqiang Zhang
- Department of Industrial Microbiology and Biotechnology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenzhao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Aihua Deng
- Department of Industrial Microbiology and Biotechnology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhaopeng Sun
- Department of Industrial Microbiology and Biotechnology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yun Zhang
- Department of Industrial Microbiology and Biotechnology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yong Liang
- Department of Industrial Microbiology and Biotechnology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yongsheng Che
- Department of Natural Products Chemistry, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Tingyi Wen
- Department of Industrial Microbiology and Biotechnology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Wang Y, Weng J, Waseem R, Yin X, Zhang R, Shen Q. Bacillus subtilis genome editing using ssDNA with short homology regions. Nucleic Acids Res 2012; 40:e91. [PMID: 22422839 PMCID: PMC3384351 DOI: 10.1093/nar/gks248] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this study, we developed a simple and efficient Bacillus subtilis genome editing method in which targeted gene(s) could be inactivated by single-stranded PCR product(s) flanked by short homology regions and in-frame deletion could be achieved by incubating the transformants at 42°C. In this process, homologous recombination (HR) was promoted by the lambda beta protein synthesized under the control of promoter PRM in the lambda cI857 PRM–PR promoter system on a temperature sensitive plasmid pWY121. Promoter PR drove the expression of the recombinase gene cre at 42°C for excising the floxed (lox sites flanked) disruption cassette that contained a bleomycin resistance marker and a heat inducible counter-selectable marker (hewl, encoding hen egg white lysozyme). Then, we amplified the single-stranded disruption cassette using the primers that carried 70 nt homology extensions corresponding to the regions flanking the target gene. By transforming the respective PCR products into the B. subtilis that harbored pWY121 and incubating the resultant mutants at 42°C, we knocked out multiple genes in the same genetic background with no marker left. This process is simple and efficient and can be widely applied to large-scale genome analysis of recalcitrant Bacillus species.
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Affiliation(s)
- Yang Wang
- Department of Plant Nutrition, College of Resource and Environmental Sciences, Nanjing Agricultural University, No.1 Weigang Road, Nanjing 210095, Jiangsu Province, PR China
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Complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for industrial production of guanosine and ribavirin. J Bacteriol 2011; 193:3142-3. [PMID: 21515778 DOI: 10.1128/jb.00440-11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Here, we report the complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for industrial production of guanosine and synthesis of ribavirin by assimilation of formamide. Comparison of its genome sequence with those of strains DSM7 and FZB42 revealed horizontal gene transfer represented by unique prophages and restriction-modification systems and indicated significant accumulation of guanosine.
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