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Zhu J, Wang X, Zhao J, Ji F, Zeng J, Wei Y, Xu L, Dong G, Ma X, Wang C. Genomic characterization and related functional genes of γ- poly glutamic acid producing Bacillus subtilis. BMC Microbiol 2024; 24:125. [PMID: 38622505 PMCID: PMC11017564 DOI: 10.1186/s12866-024-03262-z] [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: 11/04/2023] [Accepted: 03/15/2024] [Indexed: 04/17/2024] Open
Abstract
γ- poly glutamic acid (γ-PGA), a high molecular weight polymer, is synthesized by microorganisms and secreted into the extracellular space. Due to its excellent performance, γ-PGA has been widely used in various fields, including food, biomedical and environmental fields. In this study, we screened natto samples for two strains of Bacillus subtilis N3378-2at and N3378-3At that produce γ-PGA. We then identified the γ-PGA synthetase gene cluster (PgsB, PgsC, PgsA, YwtC and PgdS), glutamate racemase RacE, phage-derived γ-PGA hydrolase (PghB and PghC) and exo-γ-glutamyl peptidase (GGT) from the genome of these strains. Based on these γ-PGA-related protein sequences from isolated Bacillus subtilis and 181 B. subtilis obtained from GenBank, we carried out genotyping analysis and classified them into types 1-5. Since we found B. amyloliquefaciens LL3 can produce γ-PGA, we obtained the B. velezensis and B. amyloliquefaciens strains from GenBank and classified them into types 6 and 7 based on LL3. Finally, we constructed evolutionary trees for these protein sequences. This study analyzed the distribution of γ-PGA-related protein sequences in the genomes of B. subtilis, B. velezensis and B. amyloliquefaciens strains, then the evolutionary diversity of these protein sequences was analyzed, which provided novel information for the development and utilization of γ-PGA-producing strains.
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Affiliation(s)
- Jiayue Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xue Wang
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Jianan Zhao
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Fang Ji
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Jun Zeng
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Yanwen Wei
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - LiLi Xu
- Union Biology (Shanghai) Co., Ltd, Shanghai, 201100, China
| | - Guoying Dong
- College of Global Change and Earth System Science, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Xingyuan Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Chengmin Wang
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China.
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2
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Kato H, Sakuta M, Tsunoda T, Nakashima Y, Morita H, Ogasawara Y, Dairi T. Peptide Epimerase Responsible for d-Amino Acid Introduction in Poly-γ-glutamic Acid Biosynthesis. Biomacromolecules 2024; 25:349-354. [PMID: 38095677 DOI: 10.1021/acs.biomac.3c01000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Poly-γ-glutamic acid (PGA) is a natural polymer of d- and/or l-glutamic acid (Glu) linked by isopeptide bonds. We recently showed that PGA synthetase, an enzyme complex composed of PgsB, PgsC, and PgsA, uses only l-Glu for polymerization, and d-Glu residues are introduced by peptide epimerization. However, it remains unclear which of the three enzymes is responsible for epimerization because in vitro functional characterization of the membrane-associated PgsBCA complex has never been successful. Here, we performed gene exchange experiments and showed that PgsA is responsible for the epimerization. Additionally, we identified a region in PgsA that modulates epimerization activity based on homology modeling from the recently solved structure of MslH, which showed 53% identity to PgsA. Our results suggested that d/l-ratios of the PGA product can be altered by introducing amino acid substitutions in this region, which will be useful for the production of PGA with controlled d/l-ratios.
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Affiliation(s)
- Hinata Kato
- Graduate School of Chemical Science and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Moeka Sakuta
- Graduate School of Chemical Science and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Takeshi Tsunoda
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Yu Nakashima
- Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Hiroyuki Morita
- Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Yasushi Ogasawara
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
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3
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Chen M, Chen L, Yuan D, Niu L, Hu J, Zhang X, Zhang X, Zhang Y, Zhang X, Ling P, Liu F, Zhang D. Preparation, function, and safety evaluation of a novel degradable dermal filler, the cross-linked poly-γ-glutamic acid hydrogel particles. J Biomed Mater Res B Appl Biomater 2023; 111:1407-1418. [PMID: 36930047 DOI: 10.1002/jbm.b.35245] [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: 10/08/2022] [Revised: 02/10/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023]
Abstract
Poly-γ-glutamic acid (PGA) is a naturally degradable hydrophilic linear microbial polymer with moisturizing, immunogenic, cross-linking, and hydrogel water absorption properties similar to hyaluronic acid, a biomaterial that is commonly used as a dermal filler. To explore the development feasibility of cross-linked PGA as a novel dermal filler, we studied the local skin response to PGA fillers and the effect of various cross-linking preparations on the average longevity of dermal injection. Injection site inflammation and the formation of collagen and elastin were also determined. PGA hydrogel particles prepared using 28% PGA and 10% 1,4-butanediol diglycidyl ether showed optimal filler properties, resistance to moist heat sterilization, and an average filling longevity of 94.7 ± 61.6 days in the dermis of rabbit ears. Local redness and swelling due to filler injection recovered within 14.2 ± 3.6 days. Local tissue necrosis or systemic allergic reactions were not observed, and local collagen formation was promoted. Preliminary results suggested that dermal injection of cross-linked PGA particles appeared safe and effective, suggesting that cross-linked PGA particles could be developed as a new hydrogel dermal filler.
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Affiliation(s)
- Mian Chen
- Shandong Academy of Pharmaceutical Sciences, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide drugs, National-Local Joint Engineering Laboratory of Polysaccharide drugs, Postdoctoral Scientific Research Workstation, Jinan, China
| | - Lei Chen
- Shandong Academy of Pharmaceutical Sciences, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide drugs, National-Local Joint Engineering Laboratory of Polysaccharide drugs, Postdoctoral Scientific Research Workstation, Jinan, China
| | - Dandan Yuan
- Shandong Academy of Pharmaceutical Sciences, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide drugs, National-Local Joint Engineering Laboratory of Polysaccharide drugs, Postdoctoral Scientific Research Workstation, Jinan, China
| | - Linlin Niu
- Shandong Academy of Pharmaceutical Sciences, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide drugs, National-Local Joint Engineering Laboratory of Polysaccharide drugs, Postdoctoral Scientific Research Workstation, Jinan, China
| | - Jianting Hu
- Shandong Academy of Pharmaceutical Sciences, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide drugs, National-Local Joint Engineering Laboratory of Polysaccharide drugs, Postdoctoral Scientific Research Workstation, Jinan, China
| | - Xiaoyuan Zhang
- Shandong Academy of Pharmaceutical Sciences, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide drugs, National-Local Joint Engineering Laboratory of Polysaccharide drugs, Postdoctoral Scientific Research Workstation, Jinan, China
| | - Xiuhua Zhang
- Shandong Academy of Pharmaceutical Sciences, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide drugs, National-Local Joint Engineering Laboratory of Polysaccharide drugs, Postdoctoral Scientific Research Workstation, Jinan, China
| | - Yanyan Zhang
- Shandong Academy of Pharmaceutical Sciences, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide drugs, National-Local Joint Engineering Laboratory of Polysaccharide drugs, Postdoctoral Scientific Research Workstation, Jinan, China
| | - Xiangjun Zhang
- Shandong Academy of Pharmaceutical Sciences, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide drugs, National-Local Joint Engineering Laboratory of Polysaccharide drugs, Postdoctoral Scientific Research Workstation, Jinan, China
| | - Peixue Ling
- Shandong Academy of Pharmaceutical Sciences, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide drugs, National-Local Joint Engineering Laboratory of Polysaccharide drugs, Postdoctoral Scientific Research Workstation, Jinan, China.,School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Fei Liu
- Shandong Academy of Pharmaceutical Sciences, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide drugs, National-Local Joint Engineering Laboratory of Polysaccharide drugs, Postdoctoral Scientific Research Workstation, Jinan, China.,School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Daizhou Zhang
- Shandong Academy of Pharmaceutical Sciences, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide drugs, National-Local Joint Engineering Laboratory of Polysaccharide drugs, Postdoctoral Scientific Research Workstation, Jinan, China
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4
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Hoffmann K, Halmschlag B, Briel S, Sieben M, Putri S, Fukusaki E, Blank LM, Büchs J. Online measurement of the viscosity in shake flasks enables monitoring of γ-PGA production in depolymerase knockout mutants of Bacillus subtilis with the phosphate-starvation inducible promoter P pst. Biotechnol Prog 2023; 39:e3293. [PMID: 36081345 DOI: 10.1002/btpr.3293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/26/2022] [Accepted: 08/11/2022] [Indexed: 11/10/2022]
Abstract
Poly-γ-glutamic acid (γ-PGA) is a biopolymer with a wide range of applications, mainly produced using Bacillus strains. The formation and concomitant secretion of γ-PGA increases the culture broth viscosity, while enzymatic depolymerisation and degradation of γ-PGA decreases the culture broth viscosity. In this study, the recently published ViMOS (Viscosity Monitoring Online System) is applied for optical online measurements of broth viscosity in eight parallel shake flasks. It is shown that the ViMOS is suitable to monitor γ-PGA production and degradation online in shake flasks. This online monitoring enables the detailed analysis of the Ppst promoter and γ-PGA depolymerase knockout mutants in genetically modified Bacillus subtilis 168. The Ppst promoter becomes active under phosphate starvation. The different single depolymerase knockout mutants are ∆ggt, ∆pgdS, ∆cwlO and a triple knockout mutant. An increase in γ-PGA yield in gγ-PGA /gglucose of 190% could be achieved with the triple knockout mutant compared to the Ppst reference strain. The single cwlO knockout also increased γ-PGA production, while the other single knockouts of ggt and pgdS showed no impact. Partial depolymerisation of γ-PGA occurred despite the triple knockout. The online measured data are confirmed with offline measurements. The online viscosity system directly reflects γ-PGA synthesis, γ-PGA depolymerisation, and changes in the molecular weight. Thus, the ViMOS has great potential to rapidly gain detailed and reliable information about new strains and cultivation conditions. The broadened knowledge will facilitate the further optimization of γ-PGA production.
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Affiliation(s)
- Kyra Hoffmann
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Birthe Halmschlag
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Simon Briel
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Michaela Sieben
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Sastia Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
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5
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Abstract
Phages are viruses of bacteria and are the smallest and most common biological entities in the environment. They can reproduce immediately after infection or integrate as a prophage into their host genome. SPβ is a prophage of the Gram-positive model organism Bacillus subtilis 168, and it has been known for more than 50 years. It is sensitive to dsDNA damage and is induced through exposure to mitomycin C or UV radiation. When induced from the prophage, SPβ requires 90 min to produce and release about 30 virions. Genomes of sequenced related strains range between 128 and 140 kb, and particle-packed dsDNA exhibits terminal redundancy. Formed particles are of the Siphoviridae morphotype. Related isolates are known to infect other B. subtilis clade members. When infecting a new host, SPβ presumably follows a two-step strategy, adsorbing primarily to teichoic acid and secondarily to a yet unknown factor. Once in the host, SPβ-related phages pass through complex lysis-lysogeny decisions and either enter a lytic cycle or integrate as a dormant prophage. As prophages, SPβ-related phages integrate at the host chromosome's replication terminus, and frequently into the spsM or kamA gene. As a prophage, it imparts additional properties to its host via phage-encoded proteins. The most notable of these functional proteins is sublancin 168, which is used as a molecular weapon by the host and ensures prophage maintenance. In this review, we summarise the existing knowledge about the biology of the phage regarding its life cycle and discuss its potential as a research object.
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Affiliation(s)
- Katharina Kohm
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany
| | - Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany.
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6
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Guo J, Shi W, Li J, Zhai Z. Effects of poly-γ-glutamic acid and poly-γ-glutamic acid super absorbent polymer on the sandy loam soil hydro-physical properties. PLoS One 2021; 16:e0245365. [PMID: 33434231 PMCID: PMC7983855 DOI: 10.1371/journal.pone.0245365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/28/2020] [Indexed: 11/26/2022] Open
Abstract
The main forms of poly-γ-glutamic acid (γ-PGA) applied in agriculture include
agricultural γ-PGA and γ-PGA super absorbent polymer (SAP). Laboratory
experiments were conducted with a check treatment CK (no γ-PGA added) and two
different forms of γ-PGA added to sandy loam soil (T and TM stand for γ-PGA and
γ-PGA SAP) at four different soil mass ratios (0.05% (1), 0.10% (2), 0.15% (3)
and 0.20% (4)) to determine their effects on sandy loam soil hydro-physical
properties. Both of them could reduce the cumulative infiltration of soil water.
The total available water (TAW) which the soil water content (SWC) from field
water capacity (FC) to permanent wilting point (PWP) after γ-PGA added into
sandy loam soil had no significant different compared with CK, and the TAW was
highest at the treatment of γ-PGA with 0.10% addition amount into sandy loam
soil. However, the TAW of sandy loam soil increased dramatically with the γ-PGA
SAP addition amount increasing. TM3 had the highest soil water absorption among
the treatments with γ-PGA SAP. The T1 to T4 treatments with γ-PGA addition
slightly prolonged retention time (RT) when SWC varied from FC to PWP compared
with CK. For γ-PGA SAP addition treatments, the time for SWC varied from FC to
PWP was 1.48 times (TM1), 1.88 times (TM2), 2.01 times (TM3) and 2.87 times
(TM4) longer than that of CK, respectively. The results of this study will
provide further information for the use of these materials in agricultural
application.
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Affiliation(s)
- Jianzhong Guo
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
| | - Wenjuan Shi
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
| | - Jiake Li
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
| | - Zhongmin Zhai
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
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7
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Ogasawara Y, Shigematsu M, Sato S, Kato H, Dairi T. Involvement of Peptide Epimerization in Poly-γ-glutamic Acid Biosynthesis. Org Lett 2019; 21:3972-3975. [PMID: 31090431 DOI: 10.1021/acs.orglett.9b01121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Poly-γ-glutamic acid (PGA) is a promising polymer that comprises d- and l-glutamic acid (Glu) connected via an amide bond. PGA is biosynthesized by a transmembrane enzyme complex composed of PgsB, PgsC, and PgsA. However, the detailed reaction, especially the mechanism for introducing d-Glu residues into PGA, remains elusive. We herein report isotope tracer experiments with deuterated l- and d-Glu and demonstrate that epimerization of a growing peptide is involved in PGA biosynthesis.
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Affiliation(s)
- Yasushi Ogasawara
- Graduate School of Engineering , Hokkaido University , Sapporo , Hokkaido 060-8628 , Japan
| | - Mayuko Shigematsu
- Graduate School of Engineering , Hokkaido University , Sapporo , Hokkaido 060-8628 , Japan
| | - Shota Sato
- Graduate School of Engineering , Hokkaido University , Sapporo , Hokkaido 060-8628 , Japan
| | - Hinata Kato
- Graduate School of Engineering , Hokkaido University , Sapporo , Hokkaido 060-8628 , Japan
| | - Tohru Dairi
- Graduate School of Engineering , Hokkaido University , Sapporo , Hokkaido 060-8628 , Japan
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8
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Massaiu I, Pasotti L, Sonnenschein N, Rama E, Cavaletti M, Magni P, Calvio C, Herrgård MJ. Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains. Microb Cell Fact 2019; 18:3. [PMID: 30626384 PMCID: PMC6325765 DOI: 10.1186/s12934-018-1052-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/29/2018] [Indexed: 12/15/2022] Open
Abstract
Background Genome-scale metabolic models (GEMs) allow predicting metabolic phenotypes from limited data on uptake and secretion fluxes by defining the space of all the feasible solutions and excluding physio-chemically and biologically unfeasible behaviors. The integration of additional biological information in genome-scale models, e.g., transcriptomic or proteomic profiles, has the potential to improve phenotype prediction accuracy. This is particularly important for metabolic engineering applications where more accurate model predictions can translate to more reliable model-based strain design. Results Here we present a GEM with Enzymatic Constraints using Kinetic and Omics data (GECKO) model of Bacillus subtilis, which uses publicly available proteomic data and enzyme kinetic parameters for central carbon (CC) metabolic reactions to constrain the flux solution space. This model allows more accurate prediction of the flux distribution and growth rate of wild-type and single-gene/operon deletion strains compared to a standard genome-scale metabolic model. The flux prediction error decreased by 43% and 36% for wild-type and mutants respectively. The model additionally increased the number of correctly predicted essential genes in CC pathways by 2.5-fold and significantly decreased flux variability in more than 80% of the reactions with variable flux. Finally, the model was used to find new gene deletion targets to optimize the flux toward the biosynthesis of poly-γ-glutamic acid (γ-PGA) polymer in engineered B. subtilis. We implemented the single-reaction deletion targets identified by the model experimentally and showed that the new strains have a twofold higher γ-PGA concentration and production rate compared to the ancestral strain. Conclusions This work confirms that integration of enzyme constraints is a powerful tool to improve existing genome-scale models, and demonstrates the successful use of enzyme-constrained models in B. subtilis metabolic engineering. We expect that the new model can be used to guide future metabolic engineering efforts in the important industrial production host B. subtilis.
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Affiliation(s)
- Ilaria Massaiu
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Dep. Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy.,Centre for Health Technologies, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Lorenzo Pasotti
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Dep. Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy.,Centre for Health Technologies, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Nikolaus Sonnenschein
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Erlinda Rama
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Matteo Cavaletti
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Paolo Magni
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Dep. Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy.,Centre for Health Technologies, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Cinzia Calvio
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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9
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The Revisited Genome of Bacillus subtilis Bacteriophage SPP1. Viruses 2018; 10:v10120705. [PMID: 30544981 PMCID: PMC6316719 DOI: 10.3390/v10120705] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/06/2018] [Accepted: 12/06/2018] [Indexed: 02/05/2023] Open
Abstract
Bacillus subtilis bacteriophage SPP1 is a lytic siphovirus first described 50 years ago [1]. Its complete DNA sequence was reported in 1997 [2]. Here we present an updated annotation of the 44,016 bp SPP1 genome and its correlation to different steps of the viral multiplication process. Five early polycistronic transcriptional units encode phage DNA replication proteins and lysis functions together with less characterized, mostly non-essential, functions. Late transcription drives synthesis of proteins necessary for SPP1 viral particles assembly and for cell lysis, together with a short set of proteins of unknown function. The extensive genetic, biochemical and structural biology studies on the molecular mechanisms of SPP1 DNA replication and phage particle assembly rendered it a model system for tailed phages research. We propose SPP1 as the reference species for a new SPP1-like viruses genus of the Siphoviridae family.
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10
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Ramaswamy S, Rasheed M, Morelli CF, Calvio C, Sutton BJ, Pastore A. The structure of PghL hydrolase bound to its substrate poly-γ-glutamate. FEBS J 2018; 285:4575-4589. [PMID: 30387270 PMCID: PMC6506827 DOI: 10.1111/febs.14688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/05/2018] [Accepted: 10/30/2018] [Indexed: 11/28/2022]
Abstract
The identification of new strategies to fight bacterial infections in view of the spread of multiple resistance to antibiotics has become mandatory. It has been demonstrated that several bacteria develop poly‐γ‐glutamic acid (γ‐PGA) capsules as a protection from external insults and/or host defence systems. Among the pathogens that shield themselves in these capsules are Bacillus anthracis, Francisella tularensis and several Staphylococcus strains. These are important pathogens with a profound influence on human health. The recently characterised γ‐PGA hydrolases, which can dismantle the γ‐PGA‐capsules, are an attractive new direction that can offer real hope for the development of alternatives to antibiotics, particularly in cases of multidrug resistant bacteria. We have characterised in detail the cleaving mechanism and stereospecificity of the enzyme PghL (previously named YndL) from Bacillus subtilis encoded by a gene of phagic origin and dramatically efficient in degrading the long polymeric chains of γ‐PGA. We used X‐ray crystallography to solve the three‐dimensional structures of the enzyme in its zinc‐free, zinc‐bound and complexed forms. The protein crystallised with a γ‐PGA hexapeptide substrate and thus reveals details of the interaction which could explain the stereospecificity observed and give hints on the catalytic mechanism of this class of hydrolytic enzymes.
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Affiliation(s)
- Sneha Ramaswamy
- The Randall Centre for Cell & Molecular Biophysics, King's College London, UK
| | - Masooma Rasheed
- The Wohl Institute, King's College London, UK.,UK Dementia Research Institute at King's College London, UK
| | | | - Cinzia Calvio
- Department of Biology and Biotechnology, University of Pavia, Italy
| | - Brian J Sutton
- The Randall Centre for Cell & Molecular Biophysics, King's College London, UK
| | - Annalisa Pastore
- The Wohl Institute, King's College London, UK.,UK Dementia Research Institute at King's College London, UK.,Department of Molecular Medicine, University of Pavia, Italy
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11
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Effects of poly-gamma-glutamic acid on inflammatory and metabolic biomarkers in sleep-restricted rats. Sleep Biol Rhythms 2018. [DOI: 10.1007/s41105-018-0170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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12
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Eymard-Vernain E, Coute Y, Adrait A, Rabilloud T, Sarret G, Lelong C. The poly-gamma-glutamate of Bacillus subtilis interacts specifically with silver nanoparticles. PLoS One 2018; 13:e0197501. [PMID: 29813090 PMCID: PMC5973573 DOI: 10.1371/journal.pone.0197501] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 05/03/2018] [Indexed: 12/03/2022] Open
Abstract
For many years, silver nanoparticles, as with other antibacterial nanoparticles, have been extensively used in manufactured products. However, their fate in the environment is unclear and raises questions. We studied the fate of silver nanoparticles in the presence of bacteria under growth conditions that are similar to those found naturally in the environment (that is, bacteria in a stationary phase with low nutrient concentrations). We demonstrated that the viability and the metabolism of a gram-positive bacteria, Bacillus subtilis, exposed during the stationary phase is unaffected by 1 mg/L of silver nanoparticles. These results can be partly explained by a physical interaction of the poly-gamma-glutamate (PGA) secreted by Bacillus subtilis with the silver nanoparticles. The coating of the silver nanoparticles by the secreted PGA likely results in a loss of the bioavailability of nanoparticles and, consequently, a decrease of their biocidal effect.
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Affiliation(s)
- Elise Eymard-Vernain
- BIG, LCBM, ProMD, UMR CNRS-CEA-UGA, Grenoble, France
- ISTerre, CNRS-UGA, Grenoble, France
| | - Yohann Coute
- BIG, BGE, EDyP, INSERM-CEA-UGA, Grenoble, France
| | - Annie Adrait
- BIG, BGE, EDyP, INSERM-CEA-UGA, Grenoble, France
| | | | | | - Cécile Lelong
- BIG, LCBM, ProMD, UMR CNRS-CEA-UGA, Grenoble, France
- * E-mail:
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13
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Ghosh K, Kang HS, Hyun WB, Kim KP. High prevalence of Bacillus subtilis-infecting bacteriophages in soybean-based fermented foods and its detrimental effects on the process and quality of Cheonggukjang. Food Microbiol 2018; 76:196-203. [PMID: 30166141 DOI: 10.1016/j.fm.2018.05.007] [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] [Received: 03/21/2018] [Accepted: 05/20/2018] [Indexed: 01/12/2023]
Abstract
While the detrimental effect of bacteriophages on lactic acid bacterial fermentation is well documented, the importance of Bacillus subtilis phages in soybean-based fermented foods is not. In this study, we show for the first time that 100% of Korean soybean-based fermented foods (Doenjang, Gochujang, and Cheonggukjang) and 70% of raw materials (Meju and rice straw) were contaminated with B. subtilis-infecting phages (as high as 3.7 × 104 PFU g-1). Among 15 isolated B. subtilis-infecting phages, BSP18 was selected for further studies due to its specificity to and relatively broad host infectivity (34%) against B. subtilis. This Myoviridae family phage, BSP18 could infect all of the tested wild-type and commercially-used strains for soybean-based fermented food preparation. Furthermore, artificial contamination of as low as 102 PFU g-1 of BSP18 significantly inhibited B. subtilis growth during Cheonggukjang fermentation. Moreover, phage-treated samples contained considerably more degraded γ-PGA which could negatively affect the functional property of Cheonggukjang. We also present the data, strongly suggesting BSP18-encoded, not bacterial, γ-PGA hydrolase was responsible for γ-PGA degradation. In conclusion, B. subtilis phages are widespread in Korean soybean-based fermented foods and it should be of great concern as phages may hamper the bacterial growth during fermentation and yield poor quality products.
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Affiliation(s)
- Kuntal Ghosh
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, South Korea
| | - Hai Seong Kang
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, South Korea
| | - Woo Bin Hyun
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, South Korea
| | - Kwang-Pyo Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, South Korea.
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Ghosh K, Senevirathne A, Kang HS, Hyun WB, Kim JE, Kim KP. Complete Nucleotide Sequence Analysis of a Novel Bacillus subtilis-Infecting Bacteriophage BSP10 and Its Effect on Poly-Gamma-Glutamic Acid Degradation. Viruses 2018; 10:E240. [PMID: 29734701 PMCID: PMC5977233 DOI: 10.3390/v10050240] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/01/2018] [Accepted: 05/01/2018] [Indexed: 01/21/2023] Open
Abstract
While the harmful effects of lactic acid bacterial bacteriophages in the dairy industry are well-established, the importance of Bacillus subtilis-infecting bacteriophages on soybean fermentation is poorly-studied. In this study, we isolated a B. subtilis-infecting bacteriophage BSP10 from Meju (a brick of dried fermented soybean) and further characterized it. This Myoviridae family bacteriophage exhibited a narrow host range against B. subtilis strains (17/52, 32.7%). The genome of bacteriophage BSP10 is 153,767 bp long with 236 open reading frames and 5 tRNAs. Comparative genomics (using dot plot, progressiveMauve alignment, heat-plot, and BLASTN) and phylogenetic analysis strongly suggest its incorporation as a new species in the Nit1virus genus. Furthermore, bacteriophage BSP10 was efficient in the growth inhibition of B. subtilis ATCC 15245 in liquid culture and in Cheonggukjang (a soybean fermented food) fermentation. Artificial contamination of as low as 10² PFU/g of bacteriophage BSP10 during Cheonggukjang fermentation significantly reduced bacterial numbers by up to 112 fold in comparison to the control (no bacteriophage). Moreover, for the first time, we experimentally proved that B. subtilis-infecting bacteriophage greatly enhanced poly-γ-glutamic acid degradation during soybean fermentation, which is likely to negatively affect the functionalities of Cheonggukjang.
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Affiliation(s)
- Kuntal Ghosh
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, Korea.
| | - Amal Senevirathne
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, Korea.
| | - Hai Seong Kang
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, Korea.
| | - Woo Bin Hyun
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, Korea.
| | - Ji Eun Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, Korea.
| | - Kwang-Pyo Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, Korea.
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Shah Mahmud R, Garifulina KI, Ulyanova VV, Evtugyn VG, Mindubaeva LN, Khazieva LR, Dudkina EV, Vershinina VI, Kolpakov AI, Ilinskaya ON. Bacteriophages of soil bacilli: A new multivalent phage of Bacillus altitudinis. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2017. [DOI: 10.3103/s0891416817020082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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16
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Ozaki T, Abe N, Kimura K, Suzuki A, Kaneko J. Genomic analysis of Bacillus subtilis lytic bacteriophage ϕNIT1 capable of obstructing natto fermentation carrying genes for the capsule-lytic soluble enzymes poly-γ-glutamate hydrolase and levanase. Biosci Biotechnol Biochem 2016; 81:135-146. [PMID: 27885938 DOI: 10.1080/09168451.2016.1232153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bacillus subtilis strains including the fermented soybean (natto) starter produce capsular polymers consisting of poly-γ-glutamate and levan. Capsular polymers may protect the cells from phage infection. However, bacteriophage ϕNIT1 carries a γ-PGA hydrolase gene (pghP) that help it to counteract the host cell's protection strategy. ϕNIT had a linear double stranded DNA genome of 155,631-bp with a terminal redundancy of 5,103-bp, containing a gene encoding an active levan hydrolase. These capsule-lytic enzyme genes were located in the possible foreign gene cluster regions between central core and terminal redundant regions, and were expressed at the late phase of the phage lytic cycle. All tested natto origin Spounavirinae phages carried both genes for capsule degrading enzymes similar to ϕNIT1. A comparative genomic analysis revealed the diversity among ϕNIT1 and Bacillus phages carrying pghP-like and levan-hydrolase genes, and provides novel understanding on the acquisition mechanism of these enzymatic genes.
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Affiliation(s)
- Tatsuro Ozaki
- a Department of Microbial Biotechnology, Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
| | - Naoki Abe
- a Department of Microbial Biotechnology, Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
| | - Keitarou Kimura
- b Laboratory of Applied Microbiology , Food Research Institute-National Agriculture and Food Research Organization (NFRI-NARO) , Tsukuba , Japan
| | - Atsuto Suzuki
- a Department of Microbial Biotechnology, Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
| | - Jun Kaneko
- a Department of Microbial Biotechnology, Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
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