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Suwannasing W, Tanamool V, Singhaboot P, Kaewkannetra P. Valorisation of Pineapple Cannery Waste as a Cost Effective Carbon Source for Poly 3-hydroxyabutyrate (P3HB) Production. Polymers (Basel) 2023; 15:3297. [PMID: 37571191 PMCID: PMC10422540 DOI: 10.3390/polym15153297] [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: 05/06/2023] [Revised: 06/17/2023] [Accepted: 06/28/2023] [Indexed: 08/13/2023] Open
Abstract
Pineapple is one of the most important agro-industrial sugar-based fruits in Thailand. In this study, the waste stream from pineapple cannery processing was utilised and evaluated for potential use in the production of a main biopolymer group widely known as polyhydroxyalkanoates (PHAs) through aerobic batch fermentation. Firstly, pineapple cannery waste (PCW) collected from three processing sources, pineapple juice (PAJ), peel and core juice (PCJ), and pulp-washing water (PWW), was used as a carbon source. Secondly, it was characterised and pretreated. Then, batch fermentation was performed by using the optimal condition (200 rpm agitation rate, 37 °C, and fermentation time of 72 h) under two different nutrient conditions in each type of carbon source. The results revealed that PHAs were produced during 24-72 h of fermentation without any interference. The PHAs product obtained was characterised by their properties. Interestingly, GC-MS showed homopolymer of poly 3-hydroxybutyrate (P3HB) group characteristics, such as OH, CH, and C=O; meanwhile, H1 NMR analysis showed signals corresponding to CH3, CH2, and CH, respectively. Remarkably, utilising the PCW showed a high-potential cheap carbon source for the production of PHAs as well as for the treatment of wastewater from the fruit industry.
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Affiliation(s)
- Waranya Suwannasing
- Department of Intellectual Property, Ministry of Commerce, Nonthaburi 11000, Thailand;
| | - Varavut Tanamool
- Chemistry Program, Faculty of Science and Technology, Nakhon Ratchasima Rajabhat University, Nakhon Ratchasima 30000, Thailand;
| | - Pakjirat Singhaboot
- Faculty of Agricultural Product Innovation and Technology, Srinakharinwirot University, Nakhon Nayok 26120, Thailand;
| | - Pakawadee Kaewkannetra
- Department of Biotechnology, Faculty of Technology, Khon Kaen Univerisity, Khon Kaen 40002, Thailand
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2
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Metabolic Engineering of Bacillus megaterium for the Production of β-alanine. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0077-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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3
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Huang Y, Zhang M, Wang J, Xu D, Zhong C. Engineering microbial systems for the production and functionalization of biomaterialsBiomaterials engineering with microorganisms. Curr Opin Microbiol 2022; 68:102154. [PMID: 35568018 DOI: 10.1016/j.mib.2022.102154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/16/2022] [Accepted: 04/06/2022] [Indexed: 11/03/2022]
Abstract
A new trend in biomaterials synthesis is harnessing the production of microorganisms, owing to the low cost and sustainability. Because microorganisms use DNA as a production code, it is possible for humans to reprogram these cells and thus build living factories for the production of biomaterials. Over the past decade, advances in genetic engineering have enabled the development of various intriguing biomaterials with useful properties, with commercially available biomaterials representing only a few of these. In this review, we discuss the common strategies for the production of bulk and commodity biogenic polymers, and highlight several notable approaches such as modular protein engineering and pathway optimization in achieving these goals. We finally investigate the available synthetic biology tools that allow engineering of living materials, and discuss how this emerging class of materials has expanded the application scope of biomaterials.
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Affiliation(s)
- Yuanyuan Huang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Cas Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Mingyi Zhang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Cas Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jie Wang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Cas Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China; Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China
| | - Dake Xu
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China; Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China
| | - Chao Zhong
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Cas Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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4
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Soda N, Gonzaga ZJ, Pannu AS, Kashaninejad N, Kline R, Salomon C, Nguyen NT, Sonar P, Rehm BHA, Shiddiky MJA. Electrochemical Detection of Global DNA Methylation Using Biologically Assembled Polymer Beads. Cancers (Basel) 2021; 13:3787. [PMID: 34359688 PMCID: PMC8345084 DOI: 10.3390/cancers13153787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022] Open
Abstract
DNA methylation is a cell-type-specific epigenetic marker that is essential for transcriptional regulation, silencing of repetitive DNA and genomic imprinting. It is also responsible for the pathogenesis of many diseases, including cancers. Herein, we present a simple approach for quantifying global DNA methylation in ovarian cancer patient plasma samples based on a new class of biopolymer nanobeads. Our approach utilises the immune capture of target DNA and electrochemical quantification of global DNA methylation level within the targets in a three-step strategy that involves (i) initial preparation of target single-stranded DNA (ss-DNA) from the plasma of the patients' samples, (ii) direct adsorption of polymer nanobeads on the surface of a bare screen-printed gold electrode (SPE-Au) followed by the immobilisation of 5-methylcytosine (5mC)-horseradish peroxidase (HRP) antibody, and (iii) immune capture of target ss-DNA onto the electrode-bound PHB/5mC-HRP antibody conjugates and their subsequent qualification using the hydrogen peroxide/horseradish peroxidase/hydroquinone (H2O2/HRP/HQ) redox cycling system. In the presence of methylated DNA, the enzymatically produced (in situ) metabolites, i.e., benzoquinone (BQ), binds irreversibly to cellular DNA resulting in the unstable formation of DNA adducts and induced oxidative DNA strand breakage. These events reduce the available BQ in the system to support the redox cycling process and sequel DNA saturation on the platform, subsequently causing high Coulombic repulsion between BQ and negatively charged nucleotide strands. Thus, the increase in methylation levels on the electrode surface is inversely proportional to the current response. The method could successfully detect as low as 5% methylation level. In addition, the assay showed good reproducibility (% RSD ≤ 5%) and specificity by analysing various levels of methylation in cell lines and plasma DNA samples from patients with ovarian cancer. We envision that our bioengineered polymer nanobeads with high surface modification versatility could be a useful alternative platform for the electrochemical detection of varying molecular biomarkers.
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Affiliation(s)
- Narshone Soda
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia;
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; (N.K.); (N.-T.N.)
| | - Zennia Jean Gonzaga
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery (GRIDD), Griffith University, Nathan, QLD 4111, Australia;
| | - Amandeep Singh Pannu
- Centre for Material Science, School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD 4001, Australia; (A.S.P.); (P.S.)
- Centre for Biomedical Technologies, School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD 4001, Australia
| | - Navid Kashaninejad
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; (N.K.); (N.-T.N.)
| | - Richard Kline
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Ochsner Clinic Foundation, New Orleans, LA 70121, USA;
| | - Carlos Salomon
- Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Ochsner Clinic Foundation, New Orleans, LA 70121, USA;
- Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women’s Hospital, The University of Queensland, Brisbane, QLD 4029, Australia
- Departamento de Investigación, Postgrado y Educación Continua (DIPEC), Facultad de Ciencias de la Salud, Universidad Pedro de Valdivia, Santiago 8320000, Chile
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; (N.K.); (N.-T.N.)
| | - Prashant Sonar
- Centre for Material Science, School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD 4001, Australia; (A.S.P.); (P.S.)
- Centre for Biomedical Technologies, School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD 4001, Australia
| | - Bernd H. A. Rehm
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery (GRIDD), Griffith University, Nathan, QLD 4111, Australia;
- Menzies Health Institute Queensland (MHIQ), Griffith University, Gold Coast Campus, Gold Coast, QLD 4222, Australia
| | - Muhammad J. A. Shiddiky
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia;
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; (N.K.); (N.-T.N.)
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The "beauty in the beast"-the multiple uses of Priestia megaterium in biotechnology. Appl Microbiol Biotechnol 2021; 105:5719-5737. [PMID: 34263356 PMCID: PMC8390425 DOI: 10.1007/s00253-021-11424-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 01/05/2023]
Abstract
Abstract Over 30 years, the Gram-positive bacterium Priestia megaterium (previously known as Bacillus megaterium) was systematically developed for biotechnological applications ranging from the production of small molecules like vitamin B12, over polymers like polyhydroxybutyrate (PHB) up to the in vivo and in vitro synthesis of multiple proteins and finally whole-cell applications. Here we describe the use of the natural vitamin B12 (cobalamin) producer P. megaterium for the elucidation of the biosynthetic pathway and the subsequent systematic knowledge-based development for production purposes. The formation of PHB, a natural product of P. megaterium and potential petro-plastic substitute, is covered and discussed. Further important biotechnological characteristics of P. megaterium for recombinant protein production including high protein secretion capacity and simple cultivation on value-added carbon sources are outlined. This includes the advanced system with almost 30 commercially available expression vectors for the intracellular and extracellular production of recombinant proteins at the g/L scale. We also revealed a novel P. megaterium transcription-translation system as a complementary and versatile biotechnological tool kit. As an impressive biotechnology application, the formation of various cytochrome P450 is also critically highlighted. Finally, whole cellular applications in plant protection are completing the overall picture of P. megaterium as a versatile giant cell factory. Key points • The use of Priestia megaterium for the biosynthesis of small molecules and recombinant proteins through to whole-cell applications is reviewed. • P. megaterium can act as a promising alternative host in biotechnological production processes.
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6
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Soda N, Gonzaga ZJ, Chen S, Koo KM, Nguyen NT, Shiddiky MJA, Rehm BHA. Bioengineered Polymer Nanobeads for Isolation and Electrochemical Detection of Cancer Biomarkers. ACS APPLIED MATERIALS & INTERFACES 2021; 13:31418-31430. [PMID: 34185493 DOI: 10.1021/acsami.1c05355] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Early sensitive diagnosis of cancer is critical for enhancing treatment success. We previously bioengineered multifunctional core-shell structures composed of a poly-3-hydroxybutyrate (PHB) core densely coated with protein functions for uses in bioseparation and immunodiagnostic applications. Here, we report bioengineering of Escherichia coli to self-assemble PHB inclusions that codisplay a ferritin-derived iron-binding peptide and the protein A-derived antibody-binding Z domain. The iron-binding peptide mediated surface coating with a ferrofluid imparting superparamagnetic properties, while the Z domain remained accessible for binding of cancer biomarker-specific antibodies. We demonstrated that these nanobeads can specifically bind biomarkers in complex mixtures, enabling efficient magnetic separation toward enhanced electrochemical detection of cancer biomarkers such as methylated DNA and exosomes from cancer cells. Our study revealed that superparamagnetic core-shell structures can be derived from biological self-assembly systems for uses in sensitive and specific electrochemical detection of cancer biomarkers, laying the foundation for engineering advanced nanomaterials for diverse diagnostic approaches.
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Affiliation(s)
- Narshone Soda
- School of Environment and Science, Griffith University, Nathan, Queensland 4111, Australia
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan, Queensland 4111, Australia
| | - Zennia Jean Gonzaga
- School of Environment and Science, Griffith University, Nathan, Queensland 4111, Australia
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Shuxiong Chen
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Kevin M Koo
- The University of Queensland Centre for Clinical Research (UQCCR), Herston, Queensland 4029, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan, Queensland 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Griffith University, Nathan, Queensland 4111, Australia
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan, Queensland 4111, Australia
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
- Menzies Health Institute Queensland (MHIQ), Griffith University, Gold Coast, Queensland 4222, Australia
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7
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Xie Y, Peng Q, Ji Y, Xie A, Yang L, Mu S, Li Z, He T, Xiao Y, Zhao J, Zhang Q. Isolation and Identification of Antibacterial Bioactive Compounds From Bacillus megaterium L2. Front Microbiol 2021; 12:645484. [PMID: 33841370 PMCID: PMC8024468 DOI: 10.3389/fmicb.2021.645484] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/04/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial metabolites exhibit a variety of biologically active compounds including antibacterial and antifungal activities. It is well known that Bacillus is considered to be a promising source of bioactive secondary metabolites. Most plant pathogens have an incredible ability to mutate and acquire resistance, causing major economic losses in the agricultural field. Therefore, it is necessary to use the natural antibacterial compounds in microbes to control plant pathogens. This study was conducted to investigate the bio-active compounds of Bacillus megaterium L2. According to the activity guidance of Agrobacterium tumefaciens T-37, Erwinia carotovora EC-1 and Ralstonia solanacearum RS-2, five monomeric compounds, including erucamide (1), behenic acid (2), palmitic acid (3), phenylacetic acid (4), and β-sitosterol (5), were fractionated and purified from the crude ethyl acetate extract of B. megaterium. To our knowledge, all compounds were isolated from the bacterium for the first time. To understand the antimicrobial activity of these compounds, and their minimum inhibitory concentrations (MICs) (range: 0.98∼500 μg/mL) were determined by the broth microdilution method. For the three tested pathogens, palmitic acid exhibited almost no antibacterial activity (>500 μg/mL), while erucamide had moderate antibacterial activity (MIC = 500 μg/mL). Behenic acid showed MICs of 250 μg/mL against T-37 and RS-2 strains with an antibacterial activity. β-sitosterol showed significant antimicrobial activity against RS-2. β-sitosterol showed remarkable antimicrobial activity against RS-2 with an MIC of 15.6 μg/mL. In addition, with the antimicrobial activity, against T-37 (62.5 μg/mL) and against EC-1 (125 μg/mL) and RS-2 (15.6 μg/mL) strains notably, phenylacetic acid may be interesting for the prevention and control of phytopathogenic bacteria. Our findings suggest that isolated compounds such as behenic acid, β-sitosterol, and phenylacetic acid may be promising candidates for natural antimicrobial agents.
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Affiliation(s)
- Yudan Xie
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Qiuju Peng
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Yuyu Ji
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Ailin Xie
- College of Life Sciences, Guizhou University, Guiyang, China
| | - Long Yang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Shuzhen Mu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Zhu Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Tengxia He
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Yang Xiao
- Institution of Supervision and Inspection Product Quality of Guizhou Province, Guiyang, China
| | - Jinyi Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Qinyu Zhang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
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8
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Rami Reddy Tadi S, Dutt Ravindran S, Balakrishnan R, Sivaprakasam S. Recombinant production of poly-(3-hydroxybutyrate) by Bacillus megaterium utilizing millet bran and rapeseed meal hydrolysates. BIORESOURCE TECHNOLOGY 2021; 326:124800. [PMID: 33556706 DOI: 10.1016/j.biortech.2021.124800] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
Fermentative poly-3-hydroxybutyrate (PHB) production is mainly limited by the cost of raw material. In this present study, low-cost feedstock viz., millet bran residue (MBRH) and rapeseed meal hydrolysates were successfully utilized for PHB production. Metabolic engineering of Bacillus megaterium by co-expression of both precursor (phbRBC) and NADPH cofactor regeneration (zwf) genes resulted in 2.67-fold enhancement in PHB accumulation compared to wild strain. Modified logistic model characterized B.megaterium growth and PHB production effectively. The kinetic analysis proved that maximum cell concentration (15.01 g.L-1) and growth-associated constant (0.22 g.g-1) were found to be higher for initial MBRH concentration (S0 = 20 g.L-1). PHB production kinetics elucidated its expression in B.megaterium was growth-associated. PHB synthesized by B.megaterium was characterized using FTIR, NMR, XRD, DSC/TGA, FESEM and the physio-chemical properties enumerated its as a potential biodegradable plastic for industrial application.
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Affiliation(s)
- Subbi Rami Reddy Tadi
- BioPAT Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Som Dutt Ravindran
- Department of Biotechnology, Manipal Institute of Technology, Manipal 576104, Karnataka, India
| | - Rengesh Balakrishnan
- Department of Pharmaceutical Technology, Mahendra Engineering College, Namakkal District 637503, Tamil Nadu, India
| | - Senthilkumar Sivaprakasam
- BioPAT Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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9
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Nehru G, Tadi SRR, Sivaprakasam S. Application of Dual Promoter Expression System for the Enhanced Heparosan Production in Bacillus megaterium. Appl Biochem Biotechnol 2021; 193:2389-2402. [PMID: 33686628 DOI: 10.1007/s12010-021-03541-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/26/2021] [Indexed: 10/22/2022]
Abstract
Heparosan, a capsular polysaccharide synthesized by certain pathogenic bacteria, is a promising precursor for heparin production. Heparosan production is catalyzed by the formation of KfiC-KfiA complex and the subsequent action of KfiC and KfiA proteins. Polycistronic expression of kfiC and kfiA in Bacillus megaterium yielded an unbalanced expression of KfiC and KfiA proteins resulted in decreased heparosan production. In this study, dual promoter plasmid system was constructed to increase the expression levels of KfiC and KfiA proteins. Dual promoter plasmid system along with UDP-glucuronic acid pathway overexpression (CADuet-DB) increased the heparosan production to 203 mg/L in shake flask experiments. Batch fermentation of strain CADuet-DB under controlled conditions yielded a maximum heparosan concentration of 627 mg/L, which is 59% higher than strain CA-DB. A modified logistic model is applied to describe the kinetics of heparosan production and biomass growth. Fed batch fermentation resulted in 3-fold enhancement in heparosan concentration (1.96 g/L), compared to batch fermentation. Nuclear magnetic resonance analysis revealed that heparosan from strain CADuet-DB was similar to Escherichia coli K5 heparosan. These results suggested that dual promoter expression system is a promising alternative to polycistronic expression system to produce heparosan in B. megaterium.
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Affiliation(s)
- Ganesh Nehru
- Bioprocess Analytical Technology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Subbi Rami Reddy Tadi
- Bioprocess Analytical Technology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Senthilkumar Sivaprakasam
- Bioprocess Analytical Technology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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10
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Nduko JM, Taguchi S. Microbial Production of Biodegradable Lactate-Based Polymers and Oligomeric Building Blocks From Renewable and Waste Resources. Front Bioeng Biotechnol 2021; 8:618077. [PMID: 33614605 PMCID: PMC7889595 DOI: 10.3389/fbioe.2020.618077] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/17/2020] [Indexed: 12/20/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are naturally occurring biopolymers produced by microorganisms. PHAs have become attractive research biomaterials in the past few decades owing to their extensive potential industrial applications, especially as sustainable alternatives to the fossil fuel feedstock-derived products such as plastics. Among the biopolymers are the bioplastics and oligomers produced from the fermentation of renewable plant biomass. Bioplastics are intracellularly accumulated by microorganisms as carbon and energy reserves. The bioplastics, however, can also be produced through a biochemistry process that combines fermentative secretory production of monomers and/or oligomers and chemical synthesis to generate a repertoire of biopolymers. PHAs are particularly biodegradable and biocompatible, making them a part of today's commercial polymer industry. Their physicochemical properties that are similar to those of petrochemical-based plastics render them potential renewable plastic replacements. The design of efficient tractable processes using renewable biomass holds key to enhance their usage and adoption. In 2008, a lactate-polymerizing enzyme was developed to create new category of polyester, lactic acid (LA)-based polymer and related polymers. This review aims to introduce different strategies including metabolic and enzyme engineering to produce LA-based biopolymers and related oligomers that can act as precursors for catalytic synthesis of polylactic acid. As the cost of PHA production is prohibitive, the review emphasizes attempts to use the inexpensive plant biomass as substrates for LA-based polymer and oligomer production. Future prospects and challenges in LA-based polymer and oligomer production are also highlighted.
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Affiliation(s)
- John Masani Nduko
- Department of Dairy and Food Science and Technology, Faculty of Agriculture, Egerton University, Egerton, Kenya
| | - Seiichi Taguchi
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences and Agriculture, Tokyo University of Agriculture, Tokyo, Japan
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11
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Production and characterization of low molecular weight heparosan in Bacillus megaterium using Escherichia coli K5 glycosyltransferases. Int J Biol Macromol 2020; 160:69-76. [DOI: 10.1016/j.ijbiomac.2020.05.159] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 01/31/2023]
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12
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Diallo M, Kint N, Monot M, Collas F, Martin-Verstraete I, van der Oost J, Kengen SWM, López-Contreras AM. Transcriptomic and Phenotypic Analysis of a spoIIE Mutant in Clostridium beijerinckii. Front Microbiol 2020; 11:556064. [PMID: 33042064 PMCID: PMC7522474 DOI: 10.3389/fmicb.2020.556064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/20/2020] [Indexed: 11/26/2022] Open
Abstract
SpoIIE is a phosphatase involved in the activation of the first sigma factor of the forespore, σ F , during sporulation. A ΔspoIIE mutant of Clostridium beijerinckii NCIMB 8052, previously generated by CRISPR-Cas9, did not sporulate but still produced granulose and solvents. Microscopy analysis also showed that the cells of the ΔspoIIE mutant are elongated with the presence of multiple septa. This observation suggests that in C. beijerinckii, SpoIIE is necessary for the completion of the sporulation process, as seen in Bacillus and Clostridium acetobutylicum. Moreover, when grown in reactors, the spoIIE mutant produced higher levels of solvents than the wild type strain. The impact of the spoIIE inactivation on gene transcription was assessed by comparative transcriptome analysis at three time points (4 h, 11 h and 23 h). Approximately 5% of the genes were differentially expressed in the mutant compared to the wild type strain at all time points. Out of those only 12% were known sporulation genes. As expected, the genes belonging to the regulon of the sporulation specific transcription factors (σ F , σ E , σ G , σ K ) were strongly down-regulated in the mutant. Inactivation of spoIIE also caused differential expression of genes involved in various cell processes at each time point. Moreover, at 23 h, genes involved in butanol formation and tolerance, as well as in cell motility, were up-regulated in the mutant. In contrast, several genes involved in cell wall composition, oxidative stress and amino acid transport were down-regulated. These results indicate an intricate interdependence of sporulation and stationary phase cellular events in C. beijerinckii.
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Affiliation(s)
- Mamou Diallo
- Wageningen Food and Biobased Research, Wageningen, Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Nicolas Kint
- Laboratoire Pathogènese des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France
| | - Marc Monot
- Biomics platform, C2RT, Institut Pasteur, Paris, France
| | - Florent Collas
- Wageningen Food and Biobased Research, Wageningen, Netherlands
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogènese des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France
- Institut Universitaire de France, Paris, France
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
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13
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Godard T, Zühlke D, Richter G, Wall M, Rohde M, Riedel K, Poblete-Castro I, Krull R, Biedendieck R. Metabolic Rearrangements Causing Elevated Proline and Polyhydroxybutyrate Accumulation During the Osmotic Adaptation Response of Bacillus megaterium. Front Bioeng Biotechnol 2020; 8:47. [PMID: 32161752 PMCID: PMC7053513 DOI: 10.3389/fbioe.2020.00047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/21/2020] [Indexed: 12/15/2022] Open
Abstract
For many years now, Bacillus megaterium serves as a microbial workhorse for the high-level production of recombinant proteins in the g/L-scale. However, efficient and stable production processes require the knowledge of the molecular adaptation strategies of the host organism to establish optimal environmental conditions. Here, we interrogated the osmotic stress response of B. megaterium using transcriptome, proteome, metabolome, and fluxome analyses. An initial transient adaptation consisted of potassium import and glutamate counterion synthesis. The massive synthesis of the compatible solute proline constituted the second longterm adaptation process. Several stress response enzymes involved in iron scavenging and reactive oxygen species (ROS) fighting proteins showed higher levels under prolonged osmotic stress induced by 1.8 M NaCl. At the same time, the downregulation of the expression of genes of the upper part of glycolysis resulted in the activation of the pentose phosphate pathway (PPP), generating an oversupply of NADPH. The increased production of lactate accompanied by the reduction of acetate secretion partially compensate for the unbalanced (NADH/NAD+) ratio. Besides, the tricarboxylic acid cycle (TCA) mainly supplies the produced NADH, as indicated by the higher mRNA and protein levels of involved enzymes, and further confirmed by 13C flux analyses. As a consequence of the metabolic flux toward acetyl-CoA and the generation of an excess of NADPH, B. megaterium redirected the produced acetyl-CoA toward the polyhydroxybutyrate (PHB) biosynthetic pathway accumulating around 30% of the cell dry weight (CDW) as PHB. This direct relation between osmotic stress and intracellular PHB content has been evidenced for the first time, thus opening new avenues for synthesizing this valuable biopolymer using varying salt concentrations under non-limiting nutrient conditions.
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Affiliation(s)
- Thibault Godard
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Daniela Zühlke
- Institute of Microbiology, Universität Greifswald, Greifswald, Germany
| | - Georg Richter
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Melanie Wall
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Katharina Riedel
- Institute of Microbiology, Universität Greifswald, Greifswald, Germany
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Rainer Krull
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Braunschweig, Germany
| | - Rebekka Biedendieck
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
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14
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Chanasit W, Gonzaga ZJC, Rehm BHA. Analysis of the alginate O-acetylation machinery in Pseudomonas aeruginosa. Appl Microbiol Biotechnol 2020; 104:2179-2191. [PMID: 31900562 DOI: 10.1007/s00253-019-10310-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 11/06/2019] [Accepted: 12/08/2019] [Indexed: 12/11/2022]
Abstract
O-acetylation of alginate produced by the opportunistic human pathogen Pseudomonas aeruginosa significantly contributes to its pathogenesis. Three proteins, AlgI, AlgJ and AlgF have been implicated to form a complex and act together with AlgX for O-acetylation of alginate. AlgI was proposed to transfer the acetyl group across the cytoplasmic membrane, while periplasmic AlgJ was hypothesised to transfer the acetyl group to AlgX that acetylates alginate. To elucidate the proposed O-acetylation multiprotein complex, isogenic knockout mutants of algI, algJ and algF genes were generated in the constitutively alginate overproducing P. aeruginosa PDO300 to enable mutual stability studies. All knockout mutants were O-acetylation negative and complementation with the respective genes in cis or trans restored O-acetylation of alginate. Interestingly, only the AlgF deletion impaired alginate production suggesting a link to the alginate polymerisation/secretion multiprotein complex. Mutual stability experiments indicated that AlgI and AlgF interact independent of AlgJ as well as impact on stability of the alginate polymerisation/secretion multiprotein complex. Deletion of AlgJ did not destabilise AlgX and vice versa. When the alginate polymerase, Alg8, was absent, then AlgI and AlgF stability was strongly impaired supporting a link of the O-acetylation machinery with alginate polymerisation. Pull-down experiments suggested that AlgI interacts with AlgJ, while AlgF interacts with AlgJ and AlgI. Overall, these results suggested that AlgI-AlgJ-AlgF form a multiprotein complex linked via Alg8 to the envelope-spanning alginate polymerisation/secretion multiprotein complex to mediate O-acetylation of nascent alginate. Here, we provide the first insight on how the O-acetylation machinery is associated with alginate production.
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Affiliation(s)
- Wankuson Chanasit
- Department of Biology, Faculty of Science, Thaksin University, Pa Phayom, Patthalung, 93210, Thailand
| | - Zennia Jean C Gonzaga
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Brisbane, QLD, 4111, Australia
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Brisbane, QLD, 4111, Australia.
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15
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Aminian-Dehkordi J, Mousavi SM, Jafari A, Mijakovic I, Marashi SA. Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319. Sci Rep 2019; 9:18762. [PMID: 31822710 PMCID: PMC6904757 DOI: 10.1038/s41598-019-55041-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/21/2019] [Indexed: 12/11/2022] Open
Abstract
Bacillus megaterium is a microorganism widely used in industrial biotechnology for production of enzymes and recombinant proteins, as well as in bioleaching processes. Precise understanding of its metabolism is essential for designing engineering strategies to further optimize B. megaterium for biotechnology applications. Here, we present a genome-scale metabolic model for B. megaterium DSM319, iJA1121, which is a result of a metabolic network reconciliation process. The model includes 1709 reactions, 1349 metabolites, and 1121 genes. Based on multiple-genome alignments and available genome-scale metabolic models for other Bacillus species, we constructed a draft network using an automated approach followed by manual curation. The refinements were performed using a gap-filling process. Constraint-based modeling was used to scrutinize network features. Phenotyping assays were performed in order to validate the growth behavior of the model using different substrates. To verify the model accuracy, experimental data reported in the literature (growth behavior patterns, metabolite production capabilities, metabolic flux analysis using 13C glucose and formaldehyde inhibitory effect) were confronted with model predictions. This indicated a very good agreement between in silico results and experimental data. For example, our in silico study of fatty acid biosynthesis and lipid accumulation in B. megaterium highlighted the importance of adopting appropriate carbon sources for fermentation purposes. We conclude that the genome-scale metabolic model iJA1121 represents a useful tool for systems analysis and furthers our understanding of the metabolism of B. megaterium.
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Affiliation(s)
- Javad Aminian-Dehkordi
- Biotechnology Group, Department of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | - Seyyed Mohammad Mousavi
- Biotechnology Group, Department of Chemical Engineering, Tarbiat Modares University, Tehran, Iran.
| | - Arezou Jafari
- Department of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | - Ivan Mijakovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Sayed-Amir Marashi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.
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16
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Li R, Yang J, Xiao Y, Long L. In vivo immobilization of an organophosphorus hydrolyzing enzyme on bacterial polyhydroxyalkanoate nano-granules. Microb Cell Fact 2019; 18:166. [PMID: 31601206 PMCID: PMC6785862 DOI: 10.1186/s12934-019-1201-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 08/27/2019] [Indexed: 11/14/2022] Open
Abstract
Background Polyhydroxyalkanoate (PHA) are nano-granules naturally produced by bacteria. Two types of proteins, PHA synthase (PhaC) and phasins (PhaPs), are attached to the PHA surface by covalent and hydrophobic interactions. Utilizing these anchored proteins, functionalized PHA nano-granules displaying proteins of interest can be easily prepared by fermentation. Results In this study, a one-step fabrication method was developed for stable and efficient immobilization of an organophosphorus degrading enzyme on PHA nano-granules. The nano-biocatalysts were produced in recombinant Escherichia coli cells into which the polyhydroxyalkanoate synthesis pathway from Cupriavidus necator had been introduced. Two different strategies, covalent attachment and hydrophobic binding, were investigated by fusing bacterial organophosphorus anhydride hydrolase (OPAA4301) with PhaC and PhaP, respectively. Using both methods, the tetrameric enzyme successfully self-assembled and was displayed on the PHA surface. The display density of the target fused enzyme was enhanced to 6.8% of total protein on decorated PHA by combination of covalent and non-covalent binding modes. Immobilization of the enzyme on PHA granules resulted in higher catalytic efficiency, increased stability and excellent reusability. The kcat values of the immobilized enzymes increased by threefold compared to that of the free enzyme. The pH stability under acidic conditions was significantly enhanced, and the immobilized enzyme was stable at pH 3.0–11.0. Furthermore, more than 80% of the initial enzyme activity retained after recycling ten times. Conclusions This study provides a promising approach for cost-efficient in vivo immobilization of a tetrameric organophosphorus degrading enzyme. The immobilization process expands the utility of the enzyme, and may inspire further commercial developments of PHA nano-biocatalysts. As revealed by our results, combination of covalent and non-covalent binding is recommended for display of enzymes on PHA granules.
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Affiliation(s)
- Ru Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Jian Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Yunzhu Xiao
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China. .,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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