51
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Wang Y, Cao L, Bi M, Wang S, Chen M, Chen X, Ying M, Huang L. Wobble Editing of Cre-box by Unspecific CRISPR/Cas9 Causes CCR Release and Phenotypic Changes in Bacillus pumilus. Front Chem 2021; 9:717609. [PMID: 34434920 PMCID: PMC8381255 DOI: 10.3389/fchem.2021.717609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/30/2021] [Indexed: 11/18/2022] Open
Abstract
CRISPR-associated Cas9 endonuclease (CRISPR/Cas9) systems are widely used to introduce precise mutations, such as knocking in/out at targeted genomic sites. Herein, we successfully disrupted the transcription of multiple genes in Bacillus pumilus LG3145 using a series of unspecific guide RNAs (gRNAs) and UgRNA:Cas9 system-assisted cre-box editing. The bases used as gRNAs shared 30–70% similarity with a consensus sequence, a cis-acting element (cre-box) mediating carbon catabolite repression (CCR) of many genes in Bacillus. This triggers trans-crRNA:Cas9 complex wobble cleavage up/downstream of cre sites in the promoters of multiple genes (up to 7), as confirmed by Sanger sequencing and next-generation sequencing (NGS). LG3145 displayed an obvious CCR release phenotype, including numerous secondary metabolites released into the culture broth, ∼ 1.67 g/L white flocculent protein, pigment overflow causing orange-coloured broth (absorbance = 309 nm), polysaccharide capsules appearing outside cells, improved sugar tolerance, and a two-fold increase in cell density. We assessed the relationship between carbon catabolite pathways and phenotype changes caused by unspecific UgRNA-directed cre site wobble editing. We propose a novel strategy for editing consensus targets at operator sequences that mediates transcriptional regulation in bacteria.
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Affiliation(s)
- Yingxiang Wang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China.,Tianjin Key Laboratory of Drug Targeting and Bioimaging, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Linfeng Cao
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China.,Tianjin Key Laboratory of Drug Targeting and Bioimaging, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Meiying Bi
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China.,Tianjin Key Laboratory of Drug Targeting and Bioimaging, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Sicheng Wang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China.,Tianjin Key Laboratory of Drug Targeting and Bioimaging, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Meiting Chen
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China.,Tianjin Key Laboratory of Drug Targeting and Bioimaging, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Xingyu Chen
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China.,Tianjin Key Laboratory of Drug Targeting and Bioimaging, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Ming Ying
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China.,Tianjin Key Laboratory of Drug Targeting and Bioimaging, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Lei Huang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China.,Tianjin Key Laboratory of Drug Targeting and Bioimaging, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
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52
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Antimicrobial Peptides from Plants: A cDNA-Library Based Isolation, Purification, Characterization Approach and Elucidating Their Modes of Action. Int J Mol Sci 2021; 22:ijms22168712. [PMID: 34445412 PMCID: PMC8395713 DOI: 10.3390/ijms22168712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/19/2022] Open
Abstract
Even in a natural ecosystem, plants are continuously threatened by various microbial diseases. To save themselves from these diverse infections, plants build a robust, multilayered immune system through their natural chemical compounds. Among the several crucial bioactive compounds possessed by plants’ immune systems, antimicrobial peptides (AMPs) rank in the first tier. These AMPs are environmentally friendly, anti-pathogenic, and do not bring harm to humans. Antimicrobial peptides can be isolated in several ways, but recombinant protein production has become increasingly popular in recent years, with the Escherichia coli expression system being the most widely used. However, the efficacy of this expression system is compromised due to the difficulty of removing endotoxin from its system. Therefore, this review suggests a high-throughput cDNA library-based plant-derived AMP isolation technique using the Bacillus subtilis expression system. This method can be performed for large-scale screening of plant sources to classify unique or homologous AMPs for the agronomic and applied field of plant studies. Furthermore, this review also focuses on the efficacy of plant AMPs, which are dependent on their numerous modes of action and exceptional structural stability to function against a wide range of invaders. To conclude, the findings from this study will be useful in investigating how novel AMPs are distributed among plants and provide detailed guidelines for an effective screening strategy of AMPs.
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53
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Hemicellulosic biomass conversion by Moroccan hot spring Bacillus paralicheniformis CCMM B940 evidenced by glycoside hydrolase activities and whole genome sequencing. 3 Biotech 2021; 11:379. [PMID: 34447652 PMCID: PMC8298745 DOI: 10.1007/s13205-021-02919-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/08/2021] [Indexed: 11/05/2022] Open
Abstract
Thermophilic bacteria, especially from the genus Bacillus, constitute a huge potential source of novel enzymes that could be relevant for biotechnological applications. In this work, we described the cellulose and hemicellulose-related enzymatic activities of the hot spring Bacillus aerius CCMM B940 from the Moroccan Coordinated Collections of Microorganisms (CCMM), and revealed its potential for hemicellulosic biomass utilization. Indeed, B940 was able to degrade complex polysaccharides such as xylan and lichenan and exhibited activity towards carboxymethylcellulose. The strain was also able to grow on agriculture waste such as orange and apple peels as the sole carbon source. Whole-genome sequencing allowed the reclassification of CCMM B940 previously known as B. aerius into Bacillus paralicheniformis since the former species name has been rejected. The draft genome reported here is composed of 38 contigs resulting in a genome of 4,315,004 bp and an average G + C content of 45.87%, and is an important resource for illuminating the molecular mechanisms of carbohydrate metabolism. The annotated genomic sequences evidenced more than 52 genes encoding glycoside hydrolases and pectate lyases belonging to 27 different families of CAZymes that are involved in the degradation of plant cell wall carbohydrates. Genomic predictions in addition to in vitro experiments have revealed broad hydrolytic capabilities of the strain, thus reinforcing its relevance for biotechnology applications.
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54
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Appelbaum M, Schweder T. Metabolic Engineering of
Bacillus
– New Tools, Strains, and Concepts. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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55
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Li M, Zhu W, Meng Q, Miao M, Zhang T. Characterization of xylitol 4-dehydrogenase from Erwinia aphidicola and its co-expression with NADH oxidase in Bacillus subtilis. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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56
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Ouyang X, Liu Y, Qu R, Tian M, Yang T, Zhu R, Gao H, Jin M, Huang J. Optimizing Protein-Glutaminase Expression in Bacillus subtilis. Curr Microbiol 2021; 78:1752-1762. [PMID: 33740115 DOI: 10.1007/s00284-021-02404-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/10/2021] [Indexed: 10/21/2022]
Abstract
Protein-glutaminase (PG) is a promising protein deaminase. It only hydrolyzes the side chain amido groups of protein-bound to generate ammonia and protein-L-glutamic acid and does not catalyze any other undesirable changes in protein structures. Deamidation of proteins via PG can influence the solubility, emulsification, foaming, and gelation properties of proteins, which are important properties for some food proteins. Therefore, there is great potential for the application of PG in the food industry. PG is derived from Chryseobacterium proteolyticum (C. proteolyticum); however, wild strains are difficult to industrialize because of their low levels of enzyme production. In this article, we studied different strategies for PG expression in B. subtilis. Results showed that PG produced from C. proteolyticum could be successfully secreted in B. subtilis WB800N, and actively secreted in B. subtilis 168(BS168) or DB403 containing a pro-peptide (pro-PG). The secreted PG from B. subtilis WB800N was inactive unless digested by exogenous proteases, such as trypsin, alkaline protease, and neutral protease. However, active PG was secreted by the self-processing of BS168 and DB403. The specific activity of purified PG reached 20.9 U/mg. PG showed maximum activity at pH 5.5, 55 °C and more than 80% of PG activity was retained within a range of pH 3.5-6.5. When Cbz-Gln-Gly was used as the substrate, PG activity was 31.1 ± 0.9 μM min-1 mg-1. Mg2+, Ca2+, and Zn2+ stabilized and even activated PG activity. These strategies concerning PG expression in B. subtilis and the enzymatic properties of PG provide efficient alternatives for PG research and contribute to the industrial-scale production of PG.
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Affiliation(s)
- Xiaoying Ouyang
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, People's Republic of China
| | - Yingjie Liu
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, People's Republic of China
| | - Ruidan Qu
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, People's Republic of China
| | - Min Tian
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, People's Republic of China
| | - Ting Yang
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, People's Republic of China
| | - Rui Zhu
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, People's Republic of China
| | - Hongliang Gao
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, People's Republic of China.
| | - Mingfei Jin
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, People's Republic of China.
| | - Jing Huang
- School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, People's Republic of China.
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57
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Movahedpour A, Ahmadi N, Ghalamfarsa F, Ghesmati Z, Khalifeh M, Maleksabet A, Shabaninejad Z, Taheri-Anganeh M, Savardashtaki A. β-Galactosidase: From its source and applications to its recombinant form. Biotechnol Appl Biochem 2021; 69:612-628. [PMID: 33656174 DOI: 10.1002/bab.2137] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Carbohydrate-active enzymes are a group of important enzymes playing a critical role in the degradation and synthesis of carbohydrates. Glycosidases can hydrolyze glycosides into oligosaccharides, polysaccharides, and glycoconjugates via a cost-effective approach. Lactase is an important member of β-glycosidases found in higher plants, animals, and microorganisms. β-Galactosidases can be used to degrade the milk lactose for making lactose-free milk, which is sweeter than regular milk and is suitable for lactose-intolerant people. β-Galactosidase is employed by many food industries to degrade lactose and improve the digestibility, sweetness, solubility, and flavor of dairy products. β-Galactosidase enzymes have various families and are applied in the food-processing industries such as hydrolyzed-milk products, whey, and galactooligosaccharides. Thus, this enzyme is a valuable protein which is now produced by recombinant technology. In this review, origins, structure, recombinant production, and critical modifications of β-galactosidase for improving the production process are discussed. Since β-galactosidase is a valuable enzyme in industry and health care, a study of its various aspects is important in industrial biotechnology and applied biochemistry.
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Affiliation(s)
- Ahmad Movahedpour
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nahid Ahmadi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farideh Ghalamfarsa
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zeinab Ghesmati
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoomeh Khalifeh
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Maleksabet
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mortaza Taheri-Anganeh
- Shahid Arefian Hospital, Urmia, Iran.,Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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58
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Movahedpour A, Asadi M, Khatami SH, Taheri-Anganeh M, Adelipour M, Shabaninejad Z, Ahmadi N, Irajie C, Mousavi P. A brief overview on the application and sources of α-amylase and expression hosts properties in order to production of recombinant α-amylase. Biotechnol Appl Biochem 2021; 69:650-659. [PMID: 33655550 DOI: 10.1002/bab.2140] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/22/2021] [Indexed: 01/29/2023]
Abstract
By reducing the activation energy, enzymes accelerate the chemical reaction; therefore, they are good alternative for industrial catalysts. Amylase is a suitable enzyme as a catalyst for the chemical decomposition of starch. This enzyme is of great importance, and its production is highly profitable. α-Amylase is among the most important amylases produced naturally by animals, plants, and microorganisms. Still, the α-amylases produced by bacteria have a special place in industry and commerce. Moreover, a large volume of this enzyme can be produced by selecting an appropriate and optimized host to clone and express the α-amylase gene. The present study briefly reviews the structure, application, sources, and hosts used to produce recombinant α-amylase.
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Affiliation(s)
- Ahmad Movahedpour
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Marzieh Asadi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mortaza Taheri-Anganeh
- Shahid Arefian Hospital, Urmia, Iran.,Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Maryam Adelipour
- Department of Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nahid Ahmadi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Cambyz Irajie
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pegah Mousavi
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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59
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Ping T, Zeshun X, Penghui M, Yongchao Z. Laboratory investigation on Bacillus subtilis addition to alleviate bio-clogging for constructed wetlands. ENVIRONMENTAL RESEARCH 2021; 194:110642. [PMID: 33352184 DOI: 10.1016/j.envres.2020.110642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 06/03/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
Bio-clogging is a major problem in the operation of constructed wetlands (CWs) and is caused by accumulation of biofilm and extracellular polymeric substances (EPS) in the substrate. B. subtilis can successfully produce α-amylase and endoglucanase, which can degrade polysaccharides and, consequently, disperse the EPS. Therefore, the addition of B. subtilis was used to decrease the bio-clogging of lab-scale vertical-flow constructed wetlands (VFCW) in this study, and the feasibility and performance of VFCWs were assessed. The results indicate that the addition of B. subtilis can degrade the polysaccharides in the clogging matter and thereby increase the porosity of the substrate. The hydraulic conductivity of Column 1 (with addition) increased by six times, which was 57 times that of control (Column 2). Meanwhile, the chemical oxygen demand (COD) removal rate also increased after the addition of B. subtilis. The microbial communities show that the richness and diversity within the substrate increased after addition. The relative abundance of functional groups of chemoheterotrophy, aerobic chemoheterotrophy, as well as that connected to N cycles also increased, which implied the improvement of the pollution removal efficiency. Meanwhile, the copy number of α-amylase and endoglucanase increased significantly in Column 1 with the addition of B. subtilis, which offers further support for a hydrolase-induced reduction of polysaccharides and the efficiency of B. subtilis on bio-clogging alleviation. The results showed that B. subtilis addition is an effective and safe solution to control the bio-clogging for CWs. However, further research about long-term effect assessment and dosing strategy optimization should be conducted.
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Affiliation(s)
- Tang Ping
- The College of Material and Environment Engineering, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Xiang Zeshun
- The College of Material and Environment Engineering, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Ma Penghui
- The College of Material and Environment Engineering, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Zhou Yongchao
- The Institute of Municipal Engineering, The College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, Zhejiang, China.
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60
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Rational design of signal peptides for improved MtC1LPMO production in Bacillus amyloliquefaciens. Int J Biol Macromol 2021; 175:262-269. [PMID: 33561461 DOI: 10.1016/j.ijbiomac.2021.02.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 02/04/2021] [Accepted: 02/04/2021] [Indexed: 11/21/2022]
Abstract
A high-throughput screening system was established by employing enhanced green fluorescent protein as a screenable fusion tag to evaluate the expression and secretion of a lytic polysaccharide monooxygenase (MtC1LPMO) using 20 Sec-type signal peptides (SPs) from Bacillus amyloliquefaciens 111018. Among these, 10 SPs were found to be better than the native SP of MtC1LPMO. The protein expression and secretion levels using SP12 (MNITNWAAILQLQSMALQSISNTGTASS) were the highest among all SPs, with 4.1- and 2.1-fold increases over the native SP, respectively. Then, the amino acids of the 10 best SPs were analyzed, and the results indicated that the most abundant amino acid of the N-region was K, those of the H-region were L, F, A and V, and the C-region contained an AXA motif. Additionally, we found that the protein expression level gradually improved along with the increasing folding free energies of the SP-encoding part of the mRNA. Finally, the SPs were rationally designed to improve the expression and secretion level of MtC1LPMO. An increased positive charge of the SP N-region was found to enhance the protein expression and secretion level, as long as the folding free energy of the mRNA did not change significantly.
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61
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Suhaimi H, Dailin DJ, Malek RA, Hanapi SZ, Ambehabati KK, Keat HC, Prakasham S, Elsayed EA, Misson M, El Enshasy H. Fungal Pectinases: Production and Applications in Food Industries. Fungal Biol 2021. [DOI: 10.1007/978-3-030-64406-2_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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62
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Engineering Bacillus subtilis Cells as Factories: Enzyme Secretion and Value-added Chemical Production. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0104-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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63
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Fragment Exchange Plasmid Tools for CRISPR/Cas9-Mediated Gene Integration and Protease Production in Bacillus subtilis. Appl Environ Microbiol 2020; 87:AEM.02090-20. [PMID: 33097498 PMCID: PMC7755240 DOI: 10.1128/aem.02090-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/14/2020] [Indexed: 12/26/2022] Open
Abstract
We complemented a cloning platform with new editing plasmids that allow a quick transition from high-throughput cloning and the expression of new enzymes to the stable integration of genes for the production of enzymes through B. subtilis fermentation. We present two systems for the effective assembly cloning of any genome-editing cassette that shortens the engineering procedure to obtain the final editing constructs. The utility of the customized tools is demonstrated by disrupting Bacillus’ capacity to sporulate and by introducing the stable expression of subtilisin. The tools should be useful to engineer B. subtilis strains by a variety of recombination events to ultimately improve the application range of this industry-relevant host. Since its discovery as part of the bacterial adaptative immune system, CRISPR/Cas has emerged as the most promising tool for targeted genome editing over the past few years. Various tools for genome editing in Bacillus subtilis have recently been developed, expanding and simplifying its potential development as an industrial species. A collection of vectors compatible with high-throughput (HTP) fragment exchange (FX) cloning for heterologous expression in Escherichia coli and Bacillus was previously developed. This vector catalogue was through this work supplemented with editing plasmids for genome engineering in Bacillus by adapting two CRISPR/Cas plasmids to the cloning technology. The customized tools allow versatile editing at any chosen genomic position (single-plasmid strategy) or at a fixed genomic locus (double-plasmid strategy). The single-plasmid strategy was validated by deleting the spoIIAC gene, which has an essential role in sporulation. Using the double-plasmid strategy, we demonstrate the quick transition from plasmid-based subtilisin expression to the stable integration of the gene into the amyE locus of a seven-protease-deficient KO7 strain. The newly engineered B. subtilis strain allowed the successful production of a functional enzyme. The customized tools provide improvements to the cloning procedure, should be useful for versatile genomic engineering, and contribute to a cloning platform for a quick transition from HTP enzyme expression to production through the fermentation of industrially relevant B. subtilis and related strains. IMPORTANCE We complemented a cloning platform with new editing plasmids that allow a quick transition from high-throughput cloning and the expression of new enzymes to the stable integration of genes for the production of enzymes through B. subtilis fermentation. We present two systems for the effective assembly cloning of any genome-editing cassette that shortens the engineering procedure to obtain the final editing constructs. The utility of the customized tools is demonstrated by disrupting Bacillus’ capacity to sporulate and by introducing the stable expression of subtilisin. The tools should be useful to engineer B. subtilis strains by a variety of recombination events to ultimately improve the application range of this industry-relevant host.
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64
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Xi X, Ni K, Hao H, Shang Y, Zhao B, Qian Z. Secretory expression in Bacillus subtilis and biochemical characterization of a highly thermostable polyethylene terephthalate hydrolase from bacterium HR29. Enzyme Microb Technol 2020; 143:109715. [PMID: 33375975 DOI: 10.1016/j.enzmictec.2020.109715] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/09/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023]
Abstract
The environmental threat posed by disposal of plastic wastes has drawn extensive attention in recent years wherein polyethylene terephthalate (PET) constitutes one of the major plastic materials in the wastes. Recycling of PET wastes into reusable materials effectively overcomes its accumulation in the environment and can be achieved by mechanical, chemical, and biological processes. In comparison to the other methods, enzymatic treatment utilizing PET hydrolyzing enzymes (PETases) is environmental-friendly which avoids the use of hazardous chemicals. In this study, we report on the secretory expression in Bacillus subtilis a PETase (BhrPETase) from the bacterium HR29, a close homologue of the leaf-branch compost cutinase (LCC) with 94 % sequence identity. The expression titer of BhrPETase reached 0.66 g/L in an engineered chaperone-overexpression Bacillus subtilis strain, and the biochemical characterization of BhrPETase for the first time revealed its high hydrolyzing activity towards amorphous PET in comparison to two reported PET hydrolyzing enzymes LCC and IsPETase, which were expressed under the same expression conditions in Bacillus subtilis in our study. Most intriguingly, purified BhrPETase displayed a melting temperature as high as 101 °C. To our knowledge it is the most thermostable bacterial PETase characterized so far. The superior activity and thermostability of BhrPETase rendered it one of the most promising PETases for plastic waste recycling and bioremediation applications in the future.
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Affiliation(s)
- Xingxiang Xi
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China; China Research Center, DuPont Nutrition & Biosciences, Shanghai, 200335, China
| | - Kefeng Ni
- China Research Center, DuPont Nutrition & Biosciences, Shanghai, 200335, China
| | - Helong Hao
- China Research Center, DuPont Nutrition & Biosciences, Shanghai, 200335, China
| | - Yuepeng Shang
- China Research Center, DuPont Nutrition & Biosciences, Shanghai, 200335, China
| | - Bo Zhao
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhen Qian
- China Research Center, DuPont Nutrition & Biosciences, Shanghai, 200335, China.
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65
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Imchen M, Moopantakath J, Kumavath R, Barh D, Tiwari S, Ghosh P, Azevedo V. Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance. Front Genet 2020; 11:563975. [PMID: 33240317 PMCID: PMC7677515 DOI: 10.3389/fgene.2020.563975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
A multitude of factors, such as drug misuse, lack of strong regulatory measures, improper sewage disposal, and low-quality medicine and medications, have been attributed to the emergence of drug resistant microbes. The emergence and outbreaks of multidrug resistance to last-line antibiotics has become quite common. This is further fueled by the slow rate of drug development and the lack of effective resistome surveillance systems. In this review, we provide insights into the recent advances made in computational approaches for the surveillance of antibiotic resistomes, as well as experimental formulation of combinatorial drugs. We explore the multiple roles of antibiotics in nature and the current status of combinatorial and adjuvant-based antibiotic treatments with nanoparticles, phytochemical, and other non-antibiotics based on synergetic effects. Furthermore, advancements in machine learning algorithms could also be applied to combat the spread of antibiotic resistance. Development of resistance to new antibiotics is quite rapid. Hence, we review the recent literature on discoveries of novel antibiotic resistant genes though shotgun and expression-based metagenomics. To decelerate the spread of antibiotic resistant genes, surveillance of the resistome is of utmost importance. Therefore, we discuss integrative applications of whole-genome sequencing and metagenomics together with machine learning models as a means for state-of-the-art surveillance of the antibiotic resistome. We further explore the interactions and negative effects between antibiotics and microbiomes upon drug administration.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Jamseel Moopantakath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Purba Medinipur, India
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Ursino E, Albertini AM, Fiorentino G, Gabrieli P, Scoffone VC, Pellegrini A, Gasperi G, Di Cosimo A, Barbieri G. Bacillus subtilis as a host for mosquitocidal toxins production. Microb Biotechnol 2020; 13:1972-1982. [PMID: 32864888 PMCID: PMC7533320 DOI: 10.1111/1751-7915.13648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/23/2020] [Indexed: 02/05/2023] Open
Abstract
Aedes albopictus transmits several arboviral infections. In the absence of vaccines, control of mosquito populations is the only strategy to prevent vector-borne diseases. As part of the search for novel, biological and environmentally friendly strategies for vector control, the isolation of new bacterial species with mosquitocidal activity represents a promising approach. However, new bacterial isolates may be difficult to grow and genetically manipulate. To overcome these limits, here we set up a system allowing the expression of mosquitocidal bacterial toxins in the well-known genetic background of Bacillus subtilis. As a proof of this concept, the ability of B. subtilis to express individual or combinations of toxins of Bacillus thuringiensis israelensis (Bti) was studied. Different expression systems in which toxin gene expression was driven by IPTG-inducible, auto-inducible or toxin gene-specific promoters were developed. The larvicidal activity of the resulting B. subtilis strains against second-instar Ae. albopictus larvae allowed studying the activity of individual toxins or the synergistic interaction among Cry and Cyt toxins. The expression systems here presented lay the foundation for a better improved system to be used in the future to characterize the larvicidal activity of toxin genes from new environmental isolates.
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Affiliation(s)
- Emanuela Ursino
- Department of Biology and BiotechnologyUniversità degli Studi di PaviaPaviaItaly
| | | | - Giulia Fiorentino
- Department of Biology and BiotechnologyUniversità degli Studi di PaviaPaviaItaly
| | - Paolo Gabrieli
- Department of Biology and BiotechnologyUniversità degli Studi di PaviaPaviaItaly
- Present address:
Department of BiosciencesUniversità degli Studi di MilanoMilanoItaly
| | | | - Angelica Pellegrini
- Department of Biology and BiotechnologyUniversità degli Studi di PaviaPaviaItaly
| | - Giuliano Gasperi
- Department of Biology and BiotechnologyUniversità degli Studi di PaviaPaviaItaly
| | - Alessandro Di Cosimo
- Department of Biology and BiotechnologyUniversità degli Studi di PaviaPaviaItaly
| | - Giulia Barbieri
- Department of Biology and BiotechnologyUniversità degli Studi di PaviaPaviaItaly
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Gaber Y, Rashad B, Hussein R, Abdelgawad M, Ali NS, Dishisha T, Várnai A. Heterologous expression of lytic polysaccharide monooxygenases (LPMOs). Biotechnol Adv 2020; 43:107583. [DOI: 10.1016/j.biotechadv.2020.107583] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/20/2022]
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68
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Su Y, Liu C, Fang H, Zhang D. Bacillus subtilis: a universal cell factory for industry, agriculture, biomaterials and medicine. Microb Cell Fact 2020; 19:173. [PMID: 32883293 PMCID: PMC7650271 DOI: 10.1186/s12934-020-01436-8] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/27/2020] [Indexed: 12/18/2022] Open
Abstract
Due to its clear inherited backgrounds as well as simple and diverse genetic manipulation systems, Bacillus subtilis is the key Gram-positive model bacterium for studies on physiology and metabolism. Furthermore, due to its highly efficient protein secretion system and adaptable metabolism, it has been widely used as a cell factory for microbial production of chemicals, enzymes, and antimicrobial materials for industry, agriculture, and medicine. In this mini-review, we first summarize the basic genetic manipulation tools and expression systems for this bacterium, including traditional methods and novel engineering systems. Secondly, we briefly introduce its applications in the production of chemicals and enzymes, and summarize its advantages, mainly focusing on some noteworthy products and recent progress in the engineering of B. subtilis. Finally, this review also covers applications such as microbial additives and antimicrobials, as well as biofilm systems and spore formation. We hope to provide an overview for novice researchers in this area, offering them a better understanding of B. subtilis and its applications.
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Affiliation(s)
- Yuan Su
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chuan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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69
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Tian R, Wang M, Shi J, Qin X, Guo H, Jia X, Li J, Liu L, Du G, Chen J, Liu Y. Cell-free synthesis system-assisted pathway bottleneck diagnosis and engineering in Bacillus subtilis. Synth Syst Biotechnol 2020; 5:131-136. [PMID: 32637666 PMCID: PMC7320236 DOI: 10.1016/j.synbio.2020.06.006] [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: 05/03/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 11/29/2022] Open
Abstract
Metabolic engineering is a key technology for cell factories construction by rewiring cellular resources to achieve efficient production of target chemicals. However, the existence of bottlenecks in synthetic pathway can seriously affect production efficiency, which is also one of the core issues for metabolic engineers to solve. Therefore, developing an approach for diagnosing potential metabolic bottlenecks in a faster and simpler manner is of great significance to accelerate cell factories construction. The cell-free reaction system based on cell lysates can transfer metabolic reactions from in vivo to in vitro, providing a flexible access to directly change protein and metabolite variables, thus provides a potential solution for rapid identification of bottlenecks. Here, bottleneck diagnosis of the N-acetylneuraminic acid (NeuAc) biosynthesis pathway in industrially important chassis microorganism Bacillus subtilis was performed using cell-free synthesis system. Specifically, a highly efficient B. subtilis cell-free system for NeuAc de novo synthesis was firstly constructed, which had a 305-fold NeuAc synthesis rate than that in vivo and enabled fast pathway dynamics analysis. Next, through the addition of all potential key intermediates in combination with substrate glucose respectively, it was found that insufficient phosphoenolpyruvate supply was one of the NeuAc pathway bottlenecks. Rational in vivo metabolic engineering of NeuAc-producing B. subtilis was further performed to eliminate the bottleneck. By down-regulating the expression level of pyruvate kinase throughout the growth phase or only in the stationary phase using inhibitory N-terminal coding sequences (NCSs) and growth-dependent regulatory NCSs respectively, the maximal NeuAc titer increased 2.0-fold. Our study provides a rapid method for bottleneck diagnosis, which may help to accelerate the cycle of design, build, test and learn cycle for metabolic engineering.
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Affiliation(s)
- Rongzhen Tian
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Minghu Wang
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jintian Shi
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xiaolong Qin
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Haoyu Guo
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xuanjie Jia
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Long Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Yanfeng Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
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Xia R, Yang Y, Pan X, Gao C, Yao Y, Liu X, Teame T, Zhang F, Hu J, Ran C, Zhang Z, Liu-Clarke J, Zhou Z. Improving the production of AHL lactonase AiiO-AIO6 from Ochrobactrum sp. M231 in intracellular protease-deficient Bacillus subtilis. AMB Express 2020; 10:138. [PMID: 32757095 PMCID: PMC7406587 DOI: 10.1186/s13568-020-01075-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/28/2020] [Indexed: 12/25/2022] Open
Abstract
Quorum quenching (QQ) blocks bacterial cell-to-cell communication (i.e., quorum sensing), and is a promising antipathogenic strategy to control bacterial infection via inhibition of virulence factor expression and biofilm formation. QQ enzyme AiiO-AIO6 from Ochrobactrum sp. M231 has several excellent properties and shows biotherapeutic potential against important bacterial pathogens of aquatic species. AiiO-AIO6 can be secretory expressed in Bacillus subtilis via a non-classical secretion pathway. To improve AiiO-AIO6 production, four intracellular protease-deletion mutants of B. subtilis 1A751 were constructed by individually knocking out the intracellular protease-encoding genes (tepA, ymfH, yrrN and ywpE). The AiiO-AIO6 expression plasmid pWB-AIO6BS was transformed into the B. subtilis 1A751 and its four intracellular protease-deletion derivatives. Results showed that all recombinant intracellular protease-deletion derivatives (BSΔtepA, BSΔymfH, BSΔyrrN and BSΔywpE) had a positive impact on AiiO-AIO6 production. The highest amount of AiiO-AIO6 extracellular production of BSΔywpE in shake flask reached 1416.47 U/mL/OD600, which was about 121% higher than that of the wild-type strain. Furthermore, LC-MS/MS analysis of the degrading products of 3-oxo-C8-HSL by purification of AiiO-AIO6 indicated that AiiO-AIO6 was an AHL-lactonase which hydrolyzes the lactone ring of AHLs. Phylogenetic analysis showed that AiiO-AIO6 was classified as a member of the α/β hydrolase family with a conserved "nucleophile-acid-histidine" catalytic triad. In summary, this study showed that intracellular proteases were responsible for the reduced yields of heterologous proteins and provided an efficient strategy to enhance the extracellular production of AHL lactonase AiiO-AIO6.
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71
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Irla M, Drejer EB, Brautaset T, Hakvåg S. Establishment of a functional system for recombinant production of secreted proteins at 50 °C in the thermophilic Bacillus methanolicus. Microb Cell Fact 2020; 19:151. [PMID: 32723337 PMCID: PMC7389648 DOI: 10.1186/s12934-020-01409-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 07/20/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The suitability of bacteria as microbial cell factories is dependent on several factors such as price of feedstock, product range, production yield and ease of downstream processing. The facultative methylotroph Bacillus methanolicus is gaining interest as a thermophilic cell factory for production of value-added products from methanol. The aim of this study was to expand the capabilities of B. methanolicus as a microbial cell factory by establishing a system for secretion of recombinant proteins. RESULTS Native and heterologous signal peptides were tested for secretion of α-amylases and proteases, and we have established the use of the thermostable superfolder green fluorescent protein (sfGFP) as a valuable reporter protein in B. methanolicus. We demonstrated functional production and secretion of recombinant proteases, α-amylases and sfGFP in B. methanolicus MGA3 at 50 °C and showed that the choice of signal peptide for optimal secretion efficiency varies between proteins. In addition, we showed that heterologous production and secretion of α-amylase from Geobacillus stearothermophilus enables B. methanolicus to grow in minimal medium with starch as the sole carbon source. An in silico signal peptide library consisting of 169 predicted peptides from B. methanolicus was generated and will be useful for future studies, but was not experimentally investigated any further here. CONCLUSION A functional system for recombinant production of secreted proteins at 50 °C has been established in the thermophilic B. methanolicus. In addition, an in silico signal peptide library has been generated, that together with the tools and knowledge presented in this work will be useful for further development of B. methanolicus as a host for recombinant protein production and secretion at 50 °C.
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Affiliation(s)
- Marta Irla
- Department of Biotechnology and Food Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Eivind B Drejer
- Department of Biotechnology and Food Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Trygve Brautaset
- Department of Biotechnology and Food Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Sigrid Hakvåg
- Department of Biotechnology and Food Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
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Engineering the gut microbiota to treat chronic diseases. Appl Microbiol Biotechnol 2020; 104:7657-7671. [PMID: 32696297 PMCID: PMC7484268 DOI: 10.1007/s00253-020-10771-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/18/2020] [Accepted: 07/02/2020] [Indexed: 12/21/2022]
Abstract
Gut microbes play vital roles in host health and disease. A number of commensal bacteria have been used as vectors for genetic engineering to create living therapeutics. This review highlights recent advances in engineering gut bacteria for the treatment of chronic diseases such as metabolic diseases, cancer, inflammatory bowel diseases, and autoimmune disorders. KEY POINTS: • Bacterial homing to tumors has been exploited to deliver therapeutics in mice models. • Engineered bacteria show promise in mouse models of metabolic diseases. • Few engineered bacterial treatments have advanced to clinical studies.
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73
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van Tilburg AY, van Heel AJ, Stülke J, de Kok NAW, Rueff AS, Kuipers OP. Mini Bacillus PG10 as a Convenient and Effective Production Host for Lantibiotics. ACS Synth Biol 2020; 9:1833-1842. [PMID: 32551553 PMCID: PMC7372594 DOI: 10.1021/acssynbio.0c00194] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Efficient bacterial cell factories are important for the screening and characterization of potent antimicrobial peptides such as lantibiotics. Although lantibiotic production systems have been established in Lactococcus lactis and Escherichia coli, the industrial workhorse Bacillus subtilis has been left relatively unexplored as a lantibiotic production host. Therefore, we tested different B. subtilis strains for their ability to produce lantibiotic peptides by using the subtilin modification and transport enzymes derived from the natural subtilin producer B. subtilis ATCC 6633. Our study shows that although B. subtilis ATCC 6633 and 168 are able to produce various processed lantibiotic peptides, an evident advantage of using either the 8-fold protease-deficient strain WB800 or the genome-minimized B. subtilis 168 strain PG10 is the lack of extracellular serine protease activity. Consequently, leader processing of lantibiotic precursor peptides is circumvented and thus potential toxicity toward the production host is prevented. Furthermore, PG10 provides a clean secondary metabolic background and therefore appears to be the most promising B. subtilis lantibiotic production host. We demonstrate the production of various lantibiotic precursor peptides by PG10 and show different options for their in vitro activation. Our study thus provides a convenient B. subtilis-based lantibiotic production system, which facilitates the search for novel antimicrobial peptides.
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Affiliation(s)
- Amanda Y. van Tilburg
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
| | - Auke J. van Heel
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
| | - Jörg Stülke
- Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, 37077, Germany
| | - Niels A. W. de Kok
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
| | - Anne-Stéphanie Rueff
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
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Construction of a High-Expression System in Bacillus through Transcriptomic Profiling and Promoter Engineering. Microorganisms 2020; 8:microorganisms8071030. [PMID: 32664655 PMCID: PMC7409208 DOI: 10.3390/microorganisms8071030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/26/2020] [Accepted: 07/09/2020] [Indexed: 01/24/2023] Open
Abstract
Bacillus subtilis is an ideal host for secretion and expression of foreign proteins. The promoter is one of the most important elements to facilitate the high-level production of recombinant protein. To expand the repertoire of strong promoters for biotechnological applications in Bacillus species, 14 highly transcribed genes based on transcriptome profiling of B. pumilus BA06 were selected and evaluated for their promoter strength in B. subtilis. Consequently, a strong promoter P2069 was obtained, which could drive the genes encoding alkaline protease (aprE) and green fluorescent protein (GFP) to express more efficiency by an increase of 3.65-fold and 18.40-fold in comparison with the control promoter (PaprE), respectively. Further, promoter engineering was applied to P2069, leading to a mutation promoter (P2069M) that could increase GFP expression by 3.67-fold over the wild-type promoter (P2069). Moreover, the IPTG-inducible expression systems were constructed using the lac operon based on the strong promoters of P2069 and P2069M, which could work well both in B. subtilis and B. pumilus. In this study, highly efficient expression system for Bacillus was constructed based on transcriptome data and promoter engineering, which provide not only a new option for recombinant expression in B. subtilis, but also novel genetic tool for B. pumilus.
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75
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Liu S, Wang J, Zhu Z, Shi T, Zhang YHPJ. Efficient secretory production of large-size heterologous enzymes in Bacillus subtilis: A secretory partner and directed evolution. Biotechnol Bioeng 2020; 117:2957-2968. [PMID: 32589796 DOI: 10.1002/bit.27478] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/25/2020] [Indexed: 12/20/2022]
Abstract
Secretory production of recombinant proteins provides a simple approach to the production and purification of target proteins in the enzyme industry. We developed a combined strategy for the secretory production of three large-size heterologous enzymes with a special focus on 83-kDa isoamylase (IA) from an archaeon Sulfolobus tokodaii in a bacterium Bacillus subtilis. First, a secretory protein of the B. subtilis family 5 glycoside hydrolase endoglucanase (Cel5) was used as a fusion partner, along with the NprB signal peptide, to facilitate secretory production of IA. This secretory partner strategy was effective for the secretion of two other large enzymes: family 9 glycoside hydrolase from Clostridium phytofermentas and cellodextrin phosphorylase from Clostridium thermocellum. Second, the secretion of Cel5-IA was improved by directed evolution with two novel double-layer Petri-dish-based high-throughput screening (HTS) methods. The high-sensitivity HTS relied on the detection of high-activity Cel5 on the carboxymethylcellulose/Congo-red assay. The second modest-sensitivity HTS focused on the detection of low-activity IA on the amylodextrin-I2 assay. After six rounds of HTS, a secretory Cel5-IA level was increased to 234 mg/L, 155 times the wild-type IA with the NprB signal peptide only. This combinatory strategy could be useful to enhance the secretory production of large-size heterologous proteins in B. subtilis.
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Affiliation(s)
- Shan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Juan Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ting Shi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yi-Heng P Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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Gholami M, Moghbeli M, Kafilzadeh F, Kargar M, Torbati MB, Tavizi A, Bellevile S, Hatami J, Eslami Z. Production of recombinant lethal factor of Bacillus anthracis in Bacillus subtilis. Prep Biochem Biotechnol 2020; 51:9-15. [PMID: 32393098 DOI: 10.1080/10826068.2020.1762215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Cancer is considered as a disease with high rates of mortality and morbidity. The limitations and side effects of common treatments have prompted the need for innovative cancer therapies. Furthermore, selectivity and targeting of cancer cells are crucial factors to successful treatment of cancer. One of these methods is the use of bacterial toxins including Bacillus anthracis toxin to aid cancer therapy. This toxin is composed of three polypeptides: protective factor (PA), lethal factor (LF), and edema factor (EF). PA can bind to various surface receptors of all types of human cells and it internalizes the lethal factor and edema factor subunits of the toxin in the cytosol. In the present study, we cloned and expressed the lef gene of B. anthracis as the lethal part of the toxin in Bacillus subtilis WB600 by a shuttle expression vector PHT4. The rLF made in B. subtilis is efficiently secreted by the host into the culture medium which facilitates downstream processing. The rLF can be used to study cancer treatment. Abbreviations: EF: edema factor; LF: lethal factor; PA: protective factor; rLF: recombinant lethal factor; rPAm: recombinant protective factor mutants; uPA: urokinase-type plasminogen activator; uPAR: urokinase-type plasminogen activator receptor.
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Affiliation(s)
| | - Majid Moghbeli
- Department of Biology, Islamic Azad University, Damghan, Iran
| | | | - Mohammad Kargar
- Department of Microbiology, Islamic Azad University, Jahrom, Iran
| | | | | | | | - Javad Hatami
- Department of Education, Tarbiat Modares University, Tehran, Iran
| | - Zahra Eslami
- ALHSB Health Research Institute, Cleveland, OH, USA
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Pang B, Zhou L, Cui W, Liu Z, Zhou Z. Production of a Thermostable Pullulanase in
Bacillus subtilis
by Optimization of the Expression Elements. STARCH-STARKE 2020. [DOI: 10.1002/star.202000018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Bo Pang
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University 1800 Lihu Avenue Wuxi 214122 China
| | - Li Zhou
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University 1800 Lihu Avenue Wuxi 214122 China
| | - Wenjing Cui
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University 1800 Lihu Avenue Wuxi 214122 China
| | - Zhongmei Liu
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University 1800 Lihu Avenue Wuxi 214122 China
| | - Zhemin Zhou
- The Key Laboratory of Industrial Biotechnology of Ministry of Education School of Biotechnology, Jiangnan University 1800 Lihu Avenue Wuxi 214122 China
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Engineering Bacillus subtilis as a Versatile and Stable Platform for Production of Nanobodies. Appl Environ Microbiol 2020; 86:AEM.02938-19. [PMID: 32060024 DOI: 10.1128/aem.02938-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/11/2020] [Indexed: 12/17/2022] Open
Abstract
There is a growing need for a highly stable system to allow the production of biologics for diagnoses and therapeutic interventions on demand that could be used in extreme environments. Among the variety of biologics, nanobodies (Nbs) derived from single-chain variable antibody fragments from camelids have attracted great attention in recent years due to their small size and great stability with translational potentials in whole-body imaging and the development of new drugs. Intracellular expression using the bacterium Escherichia coli has been the predominant system to produce Nbs, and this requires lengthy steps for releasing intracellular proteins for purification as well as removal of endotoxins. Lyophilized, translationally competent cell extracts have also been explored as offering portability and long shelf life, but such extracts may be difficult to scale up and suffer from batch-to-batch variability. To address these problems, we present a new system to do the following: (i) engineer the spore-forming bacterium Bacillus subtilis to secrete Nbs that can target small molecules or protein antigens on mammalian cells, (ii) immobilize Nbs containing a cellulose-binding domain on a cellulose matrix for long-term storage and small-molecule capturing, (iii) directly use Nb-containing bacterial supernatant fluid to perform protein detection on cell surfaces, and (iv) convert engineered B. subtilis to spores that are resistant to most environmental extremes. In summary, our work may open a new paradigm for using B. subtilis as an extremely stable microbial factory to produce Nbs with applications in extreme environments on demand.IMPORTANCE It is highly desirable to produce biologics for diagnoses and therapeutic interventions on demand that could be used in a variety of settings. Among the many biologics, Nbs have attracted attention due to their small size, thermal stability, and broad utility in diagnoses, therapies, and fundamental research. Nbs originate from antibodies found in camelids, and >10 companies have invested in Nbs as potential drugs. Here, we present a system using cells of the bacterium Bacillus subtilis as a versatile platform for production of Nbs and then antigen detection via customized affinity columns. Importantly, B. subtilis carrying engineered genes for Nbs can form spores, which survive for years in a desiccated state. However, upon rehydration and exposure to nutrients, spores rapidly transition to growing cells which secrete encoded Nbs, thus allowing their manufacture and purification.
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79
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Raza A, Pothula R, Abdelgaffar H, Bashir S, Jurat-Fuentes JL. Identification and functional characterization of a β-glucosidase from Bacillus tequelensis BD69 expressed in bacterial and yeast heterologous systems. PeerJ 2020; 8:e8792. [PMID: 32266116 PMCID: PMC7115751 DOI: 10.7717/peerj.8792] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/25/2020] [Indexed: 12/31/2022] Open
Abstract
Background The identification and characterization of novel β-glucosidase genes has attracted considerable attention because of their valuable use in a variety of industrial applications, ranging from biofuel production to improved digestibility of animal feed. We previously isolated a fiber-degrading strain of Bacillus tequelensis from buffalo dung samples, and the goal of the current work was to identify β-glucosidase genes in this strain. We describe the cloning and expression of a new β-glucosidase gene (Bteqβgluc) from Bacillus tequelensis strain BD69 in bacterial and yeast hosts. The recombinant Bteqβgluc were used to characterize specificity and activity parameters, and candidate active residues involved in hydrolysis of different substrates were identified through molecular docking. Methods The full length Bteqβgluc gene was cloned and expressed in Escherichia coli and Pichia pastoris cultures. Recombinant Bteqβgluc proteins were purified by immobilized metal affinity or anion exchange chromatography and used in β-glucosidase activity assays measuring hydrolysis of ρ-nitrophenyl-β-D-glucopyranoside (pNPG). Activity parameters were determined by testing relative β-glucosidase activity after incubation under different temperature and pH conditions. Candidate active residues in Bteqβgluc were identified using molecular operating environment (MOE) software. Results The cloned Bteqβgluc gene belongs to glycoside hydrolase (GH) family 4 and encoded a 54.35 kDa protein. Specific activity of the recombinant β-glucosidase was higher when expressed in P. pastoris (1,462.25 U/mg) than in E. coli (1,445.09 U/mg) hosts using same amount of enzyme. Optimum activity was detected at pH 5 and 50 °C. The activation energy (E a) was 44.18 and 45.29 kJ/mol for Bteqβgluc produced by P. pastoris and E. coli, respectively. Results from other kinetic parameter determinations, including pK a for the ionizable groups in the active site, Gibbs free energy of activation (ΔG ‡), entropy of activation (ΔS ‡), Michaelis constant (K m) and maximum reaction velocity (V max) for pNPG hydrolysis support unique kinetics and functional characteristics that may be of interest for industrial applications. Molecular docking analysis identified Glu, Asn, Phe, Tyr, Thr and Gln residues as important in protein-ligand catalytic interactions.
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Affiliation(s)
- Ahmad Raza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Pakistan Institute of Engineering & Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Ratnasri Pothula
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States of America
| | - Heba Abdelgaffar
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States of America
| | - Saira Bashir
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Pakistan Institute of Engineering & Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Juan Luis Jurat-Fuentes
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States of America
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80
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Zhang K, Su L, Wu J. Recent Advances in Recombinant Protein Production byBacillus subtilis. Annu Rev Food Sci Technol 2020; 11:295-318. [DOI: 10.1146/annurev-food-032519-051750] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacillus subtilis has become a widely used microbial cell factory for the production of recombinant proteins, especially those associated with foods and food processing. Recent advances in genetic manipulation and proteomic analysis have been used to greatly improve protein production in B. subtilis. This review begins with a discussion of genome-editing technologies and application of the CRISPR–Cas9 system to B. subtilis. A summary of the characteristics of crucial legacy strains is followed by suggestions regarding the choice of origin strain for genetic manipulation. Finally, the review analyzes the genes and operons of B. subtilis that are important for the production of secretory proteins and provides suggestions and examples of how they can be altered to improve protein production. This review is intended to promote the engineering of this valuable microbial cell factory for better recombinant protein production.
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Affiliation(s)
- Kang Zhang
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Key Laboratory of Industrial Biotechnology, Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Key Laboratory of Industrial Biotechnology, Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Key Laboratory of Industrial Biotechnology, Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
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81
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Scheidler CM, Vrabel M, Schneider S. Genetic Code Expansion, Protein Expression, and Protein Functionalization in Bacillus subtilis. ACS Synth Biol 2020; 9:486-493. [PMID: 32053368 DOI: 10.1021/acssynbio.9b00458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The site-specific chemical modification of proteins through incorporation of noncanonical amino acids enables diverse applications, such as imaging, probing, and expanding protein functions, as well as to precisely engineer therapeutics. Here we report a general strategy that allows the incorporation of noncanonical amino acids into target proteins using the amber suppression method and their efficient secretion in the biotechnological relevant expression host Bacillus subtilis. This facilitates efficient purification of target proteins directly from the supernatant, followed by their functionalization using click chemistry. We used this strategy to site-specifically introduce norbornene lysine into a single chain antibody and functionalize it with fluorophores for the detection of human target proteins.
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Affiliation(s)
- Christopher M. Scheidler
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians University Munich, Butenandtstraße 5-13, Munich, 81377, Germany
| | - Milan Vrabel
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, Prague 6, CZ-166 10, Czech Republic
| | - Sabine Schneider
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians University Munich, Butenandtstraße 5-13, Munich, 81377, Germany
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82
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Relative contributions of non-essential Sec pathway components and cell envelope-associated proteases to high-level enzyme secretion by Bacillus subtilis. Microb Cell Fact 2020; 19:52. [PMID: 32111210 PMCID: PMC7048088 DOI: 10.1186/s12934-020-01315-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 02/21/2020] [Indexed: 12/18/2022] Open
Abstract
Background Bacillus subtilis is an important industrial workhorse applied in the production of many different commercially relevant proteins, especially enzymes. Virtually all of these proteins are secreted via the general secretion (Sec) pathway. Studies from different laboratories have demonstrated essential or non-essential contributions of various Sec machinery components to protein secretion in B. subtilis. However, a systematic comparison of the impact of each individual Sec machinery component under conditions of high-level protein secretion was so far missing. Results In the present study, we have compared the contributions of non-essential Sec pathway components and cell envelope-associated proteases on the secretion efficiency of three proteins expressed at high level. This concerned the α-amylases AmyE from B. subtilis and AmyL from Bacillus licheniformis, and the serine protease BPN’ from Bacillus amyloliquefaciens. We compared the secretion capacity of mutant strains in shake flask cultures, and the respective secretion kinetics by pulse-chase labeling experiments. The results show that secDF, secG or rasP mutations severely affect AmyE, AmyL and BPN’ secretion, but the actual effect size depends on the investigated protein. Additionally, the chaperone DnaK is important for BPN’ secretion, while AmyE or AmyL secretion are not affected by a dnaK deletion. Further, we assessed the induction of secretion stress responses in mutant strains by examining AmyE- and AmyL-dependent induction of the quality control proteases HtrA and HtrB. Interestingly, the deletion of certain sip genes revealed a strong differential impact of particular signal peptidases on the magnitude of the secretion stress response. Conclusions The results of the present study highlight the importance of SecDF, SecG and RasP for protein secretion and reveal unexpected differences in the induction of the secretion stress response in different mutant strains.
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83
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Antelo-Varela M, Aguilar Suárez R, Bartel J, Bernal-Cabas M, Stobernack T, Sura T, van Dijl JM, Maaß S, Becher D. Membrane Modulation of Super-Secreting "midi Bacillus" Expressing the Major Staphylococcus aureus Antigen - A Mass-Spectrometry-Based Absolute Quantification Approach. Front Bioeng Biotechnol 2020; 8:143. [PMID: 32185169 PMCID: PMC7059095 DOI: 10.3389/fbioe.2020.00143] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/12/2020] [Indexed: 01/18/2023] Open
Abstract
Bacillus subtilis has been extensively used as a microbial cell factory for industrial enzymes due to its excellent capacities for protein secretion and large-scale fermentation. This bacterium is also an attractive host for biopharmaceutical production. However, the secretion potential of this organism is not fully utilized yet, mostly due to a limited understanding of critical rearrangements in the membrane proteome upon high-level protein secretion. Recently, it was shown that bottlenecks in heterologous protein secretion can be resolved by genome minimization. Here, we present for the first time absolute membrane protein concentrations of a genome-reduced B. subtilis strain ("midiBacillus") expressing the immunodominant Staphylococcus aureus antigen A (IsaA). We quantitatively characterize the membrane proteome adaptation of midiBacillus during production stress on the level of molecules per cell for more than 400 membrane proteins, including determination of protein concentrations for ∼61% of the predicted transporters. We demonstrate that ∼30% of proteins with unknown functions display a significant increase in abundance, confirming the crucial role of membrane proteins in vital biological processes. In addition, our results show an increase of proteins dedicated to translational processes in response to IsaA induction. For the first time reported, we provide accumulation rates of a heterologous protein, demonstrating that midiBacillus secretes 2.41 molecules of IsaA per minute. Despite the successful secretion of this protein, it was found that there is still some IsaA accumulation occurring in the cytosol and membrane fraction, leading to a severe secretion stress response, and a clear adjustment of the cell's array of transporters. This quantitative dataset offers unprecedented insights into bioproduction stress responses in a synthetic microbial cell.
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Affiliation(s)
- Minia Antelo-Varela
- Centre of Functional Genomics of Microbes, Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Rocío Aguilar Suárez
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Jürgen Bartel
- Centre of Functional Genomics of Microbes, Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Margarita Bernal-Cabas
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Tim Stobernack
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Thomas Sura
- Centre of Functional Genomics of Microbes, Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Sandra Maaß
- Centre of Functional Genomics of Microbes, Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Centre of Functional Genomics of Microbes, Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
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84
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Engineering Biology to Construct Microbial Chassis for the Production of Difficult-to-Express Proteins. Int J Mol Sci 2020; 21:ijms21030990. [PMID: 32024292 PMCID: PMC7037952 DOI: 10.3390/ijms21030990] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/28/2020] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
A large proportion of the recombinant proteins manufactured today rely on microbe-based expression systems owing to their relatively simple and cost-effective production schemes. However, several issues in microbial protein expression, including formation of insoluble aggregates, low protein yield, and cell death are still highly recursive and tricky to optimize. These obstacles are usually rooted in the metabolic capacity of the expression host, limitation of cellular translational machineries, or genetic instability. To this end, several microbial strains having precisely designed genomes have been suggested as a way around the recurrent problems in recombinant protein expression. Already, a growing number of prokaryotic chassis strains have been genome-streamlined to attain superior cellular fitness, recombinant protein yield, and stability of the exogenous expression pathways. In this review, we outline challenges associated with heterologous protein expression, some examples of microbial chassis engineered for the production of recombinant proteins, and emerging tools to optimize the expression of heterologous proteins. In particular, we discuss the synthetic biology approaches to design and build and test genome-reduced microbial chassis that carry desirable characteristics for heterologous protein expression.
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85
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Magri A, Oliveira MR, Baldo C, Tischer CA, Sartori D, Mantovani MS, Celligoi MAPC. Production of fructooligosaccharides by Bacillus subtilis natto CCT7712 and their antiproliferative potential. J Appl Microbiol 2020; 128:1414-1426. [PMID: 31891438 DOI: 10.1111/jam.14569] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/25/2019] [Accepted: 12/30/2019] [Indexed: 01/17/2023]
Abstract
AIMS Fructooligosaccharides (FOSs) known for their health properties and β-(2→6)-levan-type FOSs have shown prebiotic and immunomodulatory activities that overcome those of commercial β-(2→1)-FOSs, but costs do not favour their use. Moreover, FOSs can reach the bloodstream through the diet, and little is known about their direct effect on cells. The aim of this work was to produce high-content FOSs by Bacillus subtilis natto CCT7712 in a bioreactor using commercial sucrose and to evaluate their antiproliferative effects in OVCAR-3 cells. METHODS AND RESULTS FOS production reached 173·60 g l-1 , 0·2 vvm aeration and uncontrolled pH. Levan-type FOSs, composed of β-(2 → 6) links and mainly GF3 (6-nystose), were identified using RMN spectroscopy, FT-IR and ESI-MS. FOSs decreased the viability and proliferation of OVCAR-3 cells, and the effects were associated with an increased pro-inflammatory response by the induction of IL-8 and TNF-α, and the repression of ER-β genes. The metabolic profiles showed disruption of cellular homeostasis that can be associated with a decrease in proliferation. CONCLUSIONS The high production of levan-type FOSs from B. subtilis natto CCT7712 in a bioreactor was achieved, and they showed antiproliferative potential in OVCAR-3 cells. SIGNIFICANCE AND IMPACT OF THE STUDY FOS could be a good target for future therapeutic studies and commercial use.
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Affiliation(s)
- A Magri
- Department of Biochemistry and Biotechnology, State University of Londrina - UEL, Londrina, Brazil
| | - M R Oliveira
- Department of Biochemistry and Biotechnology, State University of Londrina - UEL, Londrina, Brazil
| | - C Baldo
- Department of Biochemistry and Biotechnology, State University of Londrina - UEL, Londrina, Brazil
| | - C A Tischer
- Department of Biochemistry and Biotechnology, State University of Londrina - UEL, Londrina, Brazil
| | - D Sartori
- Department of Biochemistry and Biotechnology, State University of Londrina - UEL, Londrina, Brazil
| | - M S Mantovani
- Department of General Biology, State University of Londrina - UEL, Londrina, Brazil
| | - M A P C Celligoi
- Department of Biochemistry and Biotechnology, State University of Londrina - UEL, Londrina, Brazil
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86
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Utilization of Bacillus subtilis cells displaying a glucose-tolerant β-glucosidase for whole-cell biocatalysis. Enzyme Microb Technol 2020; 132:109444. [DOI: 10.1016/j.enzmictec.2019.109444] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 11/22/2022]
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87
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Tao Z, Fu G, Wang S, Jin Z, Wen J, Zhang D. Hyper-secretion mechanism exploration of a heterologous creatinase in Bacillus subtilis. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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88
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Wu J, Abbas HMK, Li J, Yuan Y, Liu Y, Wang G, Dong W. Cell Membrane-Interrupting Antimicrobial Peptides from Isatis indigotica Fortune Isolated by a Bacillus subtilis Expression System. Biomolecules 2019; 10:E30. [PMID: 31878275 PMCID: PMC7023251 DOI: 10.3390/biom10010030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/16/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023] Open
Abstract
The situation of drug resistance has become more complicated due to the scarcity of plant resistance genes, and overcoming this challenge is imperative. Isatis indigotica has been used for the treatment of wounds, viral infections, and inflammation for centuries. Antimicrobial peptides (AMPs) are found in all classes of life ranging from prokaryotes to eukaryotes. To identify AMPs, I. indigotica was explored using a novel, sensitive, and high-throughput Bacillus subtilis screening system. We found that IiR515 and IiR915 exhibited significant antimicrobial activities against a variety of bacterial (Xanthomonas oryzae, Ralstonia solanacearum, Clavibacter michiganensis, and C. fangii) and fungal (Phytophthora capsici and Botrytis cinerea) pathogens. Scanning electron microscope and cytometric analysis revealed the possible mechanism of these peptides, which was to target and disrupt the bacterial cell membrane. This model was also supported by membrane fluidity and electrical potential analyses. Hemolytic activity assays revealed that these peptides may act as a potential source for clinical medicine development. In conclusion, the plant-derived novel AMPs IiR515 and IiR915 are effective biocontrol agents and can be used as raw materials in the drug discovery field.
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Affiliation(s)
- Jia Wu
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China; (J.W.); (J.L.)
| | - Hafiz Muhammad Khalid Abbas
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jiale Li
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China; (J.W.); (J.L.)
| | - Yuan Yuan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;
| | - Yunjun Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, South Street of Zhongguancun 12, Beijing 100081, China; (Y.L.); (G.W.)
| | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, South Street of Zhongguancun 12, Beijing 100081, China; (Y.L.); (G.W.)
| | - Wubei Dong
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China; (J.W.); (J.L.)
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89
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Le VD, Phan TTP, Nguyen TM, Brunsveld L, Schumann W, Nguyen HD. Using the IPTG-Inducible Pgrac212 Promoter for Overexpression of Human Rhinovirus 3C Protease Fusions in the Cytoplasm of Bacillus subtilis Cells. Curr Microbiol 2019; 76:1477-1486. [PMID: 31612259 DOI: 10.1007/s00284-019-01783-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/27/2019] [Indexed: 01/19/2023]
Abstract
Expression and secretion of recombinant proteins in the endotoxin-free bacterium, Bacillus subtilis, has been thoroughly studied, but overexpression in the cytoplasm has been limited to only a few proteins. Here, we used the robust IPTG-inducible promoter, Pgrac212, to overexpress human rhinovirus 3C protease (HRV3C) in the cytoplasm of B. subtilis cells. A novel solubility tag, the N-terminal domain of the lysS gene of B. subtilis coding for a lysyl-tRNA synthetase was placed at the N terminus with a cleavage site for the endoprotease HRV3C, followed by His-HRV3C or His-GST-HRV3C. The recombinant protease was purified by using a Ni-NTA column. In this study, the His-HRV3C and His-GST-HRV3C proteases were overexpressed in the cytoplasm of B. subtilis at 11% and 16% of the total cellular proteins, respectively. The specific protease activities were 8065 U/mg for His-HRV3C and 3623 U/mg for His-GST-HRV3C. The purified enzymes were used to cleave two different substrates followed by purification of the two different protein targets, the green fluorescent protein and the beta-galactosidase. In conclusion, the combination of an inducible promoter Pgrac212 and a solubility tag allowed the overexpression of the HRV3C protease in the cytoplasm of B. subtilis. The resulting fusion protein was purified using a nickel column and was active in cleaving target proteins to remove the fusion tags. This study offers an effective method for producing recombinant proteins in the cytoplasm of endotoxin-free bacteria.
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Affiliation(s)
- Vuong Duong Le
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
- Ho Chi Minh City University of Technology (HUTECH), 475A Dien Bien Phu Str., Binh Thanh Dist., Hochiminh, Vietnam
- Department of Microbiology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
| | - Trang Thi Phuong Phan
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
- Laboratory of Molecular Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
| | - Tri Minh Nguyen
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
- Ho Chi Minh City University of Technology (HUTECH), 475A Dien Bien Phu Str., Binh Thanh Dist., Hochiminh, Vietnam
| | - Luc Brunsveld
- Laboratory of Chemical Biology & Institute of Complex Molecular Systems, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, Netherlands
| | - Wolfgang Schumann
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
- Institute of Genetics, University of Bayreuth, 95440, Bayreuth, Germany
| | - Hoang Duc Nguyen
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam.
- Department of Microbiology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam.
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90
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Pauly M, Gawenda N, Wagner C, Fischbach P, Ramírez V, Axmann IM, Voiniciuc C. The Suitability of Orthogonal Hosts to Study Plant Cell Wall Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2019; 8:E516. [PMID: 31744209 PMCID: PMC6918405 DOI: 10.3390/plants8110516] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 12/20/2022]
Abstract
Plant cells are surrounded by an extracellular matrix that consists mainly of polysaccharides. Many molecular components involved in plant cell wall polymer synthesis have been identified, but it remains largely unknown how these molecular players function together to define the length and decoration pattern of a polysaccharide. Synthetic biology can be applied to answer questions beyond individual glycosyltransferases by reconstructing entire biosynthetic machineries required to produce a complete wall polysaccharide. Recently, this approach was successful in establishing the production of heteromannan from several plant species in an orthogonal host-a yeast-illuminating the role of an auxiliary protein in the biosynthetic process. In this review we evaluate to what extent a selection of organisms from three kingdoms of life (Bacteria, Fungi and Animalia) might be suitable for the synthesis of plant cell wall polysaccharides. By identifying their key attributes for glycoengineering as well as analyzing the glycosidic linkages of their native polymers, we present a valuable comparison of their key advantages and limitations for the production of different classes of plant polysaccharides.
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Affiliation(s)
- Markus Pauly
- Institute for Plant Cell Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.P.); (N.G.); (V.R.)
| | - Niklas Gawenda
- Institute for Plant Cell Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.P.); (N.G.); (V.R.)
| | - Christine Wagner
- Independent Junior Research Group–Designer Glycans, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Patrick Fischbach
- Institute of Synthetic Biology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Vicente Ramírez
- Institute for Plant Cell Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.P.); (N.G.); (V.R.)
| | - Ilka M. Axmann
- Institute for Synthetic Microbiology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Cătălin Voiniciuc
- Independent Junior Research Group–Designer Glycans, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
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91
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García-Ortega X, Cámara E, Ferrer P, Albiol J, Montesinos-Seguí JL, Valero F. Rational development of bioprocess engineering strategies for recombinant protein production in Pichia pastoris (Komagataella phaffii) using the methanol-free GAP promoter. Where do we stand? N Biotechnol 2019; 53:24-34. [DOI: 10.1016/j.nbt.2019.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 06/07/2019] [Accepted: 06/08/2019] [Indexed: 12/25/2022]
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92
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Fu G, Zhang S, Dong H, Chen J, Tu R, Zhang D. Enhanced production of
d
‐psicose 3‐epimerase in
Bacillus subtilis
by regulation of segmented fermentation. Biotechnol Appl Biochem 2019; 67:812-818. [DOI: 10.1002/bab.1831] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/28/2019] [Indexed: 01/22/2023]
Affiliation(s)
- Gang Fu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin People's Republic of China
- Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences Tianjin People's Republic of China
| | - Shibin Zhang
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin People's Republic of China
- Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences Tianjin People's Republic of China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin People's Republic of China
- Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences Tianjin People's Republic of China
| | - Jingqi Chen
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin People's Republic of China
- Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences Tianjin People's Republic of China
| | - Ran Tu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin People's Republic of China
- Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences Tianjin People's Republic of China
- University of Chinese Academy of Sciences Beijing People's Republic of China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin People's Republic of China
- Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences Tianjin People's Republic of China
- University of Chinese Academy of Sciences Beijing People's Republic of China
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93
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van Tilburg AY, Cao H, van der Meulen SB, Solopova A, Kuipers OP. Metabolic engineering and synthetic biology employing Lactococcus lactis and Bacillus subtilis cell factories. Curr Opin Biotechnol 2019; 59:1-7. [DOI: 10.1016/j.copbio.2019.01.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/05/2018] [Accepted: 01/16/2019] [Indexed: 12/11/2022]
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94
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Al-Marzooq F, Bayat SA, Sayyar F, Ishaq H, Nasralla H, Koutaich R, Kawas SA. Can probiotic cleaning solutions replace chemical disinfectants in dental clinics? Eur J Dent 2019; 12:532-539. [PMID: 30369799 PMCID: PMC6178676 DOI: 10.4103/ejd.ejd_124_18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Objectives: We aim to assess the antibacterial effectiveness of probiotic cleaning in a dental clinic at the University Dental Hospital Sharjah (UDHS), UAE. Materials and Methods: The current cleaning protocol of UDHS was evaluated by the surface swabbing of three dental clinics routinely cleaned using regular chemical disinfectants. Then, a new probiotic cleaning solution containing Bacillus subtilis was applied for 3 weeks in a selected clinic. Bacteria were grown onto selective culture media for colony counting from surfaces cleaned with probiotic solution compared to those obtained from the same surfaces cleaned with the regular chemical solutions. Isolates identity was confirmed by biochemical tests or polymerase chain reaction. Results: There was a significant reduction of the bacterial counts of various bacterial species (Staphylococci, Streptococci, and Gram-negative rods) from almost all the surfaces in the dental clinic after the application of the probiotic solution compared to the same surfaces cleaned with the regular chemical solutions. However, the antibiotic resistance rates were not significantly reduced within the short period of 3 weeks of using the new probiotic cleaning product. Conclusions: This study demonstrated that the use of probiotic cleaning is effective in reducing microbial growth in dental settings. This approach may be tested further to examine the long-term effect and to evaluate the opportunity of applying this novel biotechnology as part of the infection control routine in dental settings instead of the chemical disinfectants which are known to cause serious health problems. This is the first study testing the application of probiotic-based solution in dental settings.
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Affiliation(s)
- Farah Al-Marzooq
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, UAE
| | - Shahad Al Bayat
- Department of Oral and Craniofacial Health, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - Farah Sayyar
- Department of Oral and Craniofacial Health, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - Hamdah Ishaq
- Department of Oral and Craniofacial Health, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - Husain Nasralla
- Department of Oral and Craniofacial Health, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - Rayan Koutaich
- Department of Oral and Craniofacial Health, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - Sausan Al Kawas
- Department of Oral and Craniofacial Health, College of Dental Medicine, University of Sharjah, Sharjah, UAE
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95
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Sekar A, Kim M, Jeon H, Kim K. Screening and selection of bacteria inhibiting white spot syndrome virus infection to Litopenaeus vannamei. Biochem Biophys Rep 2019; 19:100663. [PMID: 31317076 PMCID: PMC6611967 DOI: 10.1016/j.bbrep.2019.100663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/16/2019] [Accepted: 06/26/2019] [Indexed: 11/30/2022] Open
Abstract
A total of 173 bacterial strains were isolated from different sources at different regions such as fermented foods, shrimp guts, sea water, mangrove water, and sediments. These bacteria were screened against white spot syndrome virus (WSSV) infection in Palaemon paucidens. Based on mortality, white spot level, and healthiness, three bacterial strains were selected and identified using 16S rRNA gene sequencing. These bacterial strains were Bacillus subtilis KA1, B. licheniformis KA2, and B. subtilis KA3. WSSV challenge test in pilot scale was conducted using Litopenaeus vannamei with B. subtilis KA1 and B. subtilis KA3. The survival ratio of shrimp was 0% for WSSV control after 17th days, 84% for B. subtilis KA1 plus WSSV after 26th days, and 28% for B. subtilis KA3 with WSSV after 26th days. B. subtilis KA1 showed good growth at 18-37 °C in with and without 3% NaCl, and therefore can be applied to aquaculture at low to high temperatures. B. subtilis KA1 produced protease and lipase which can increase digestion to shrimp; exhibited antibacterial activity against Vibrio parahaemolyticus; and significantly increased the survival of WSSV challenged shrimps.
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Affiliation(s)
- Ashokkumar Sekar
- Division of Bio-industry, The University of Suwon, Hwaseong, 18323, Republic of Korea
| | - Myungjin Kim
- Division of Bio-industry, The University of Suwon, Hwaseong, 18323, Republic of Korea
| | - Hantaek Jeon
- Aujeon Korea Co., 904, Wonmun-ro, Heungeop-myeon, Wonju-si, Gangwon-do, 26356, Republic of Korea
| | - Keun Kim
- Division of Bio-industry, The University of Suwon, Hwaseong, 18323, Republic of Korea
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96
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Natochii T, Motronenko V. Comparative Characteristics of Biotechnological Approaches to Obtaining Recombinant Human Cytokines in Bacterial Expressing Systems. INNOVATIVE BIOSYSTEMS AND BIOENGINEERING 2019. [DOI: 10.20535/ibb.2019.3.3.170150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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97
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Secretory Expression Fine-Tuning and Directed Evolution of Diacetylchitobiose Deacetylase by Bacillus subtilis. Appl Environ Microbiol 2019; 85:AEM.01076-19. [PMID: 31253675 DOI: 10.1128/aem.01076-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/24/2019] [Indexed: 12/23/2022] Open
Abstract
Diacetylchitobiose deacetylase has great application potential in the production of chitosan oligosaccharides and monosaccharides. This work aimed to achieve high-level secretory production of diacetylchitobiose deacetylase by Bacillus subtilis and perform molecular engineering to improve catalytic performance. First, we screened 12 signal peptides for diacetylchitobiose deacetylase secretion in B. subtilis, and the signal peptide YncM achieved the highest extracellular diacetylchitobiose deacetylase activity of 13.5 U/ml. Second, by replacing the HpaII promoter with a strong promoter, the P43 promoter, the activity was increased to 18.9 U/ml. An unexpected mutation occurred at the 5' untranslated region of plasmid, and the extracellular activity reached 1,548.1 U/ml, which is 82 times higher than that of the original strain. Finally, site-directed saturation mutagenesis was performed for the molecular engineering of diacetylchitobiose deacetylase to further improve the catalytic efficiency. The extracellular activity of mutant diacetylchitobiose deacetylase R157T reached 2,042.8 U/ml in shake flasks. Mutant R157T exhibited much higher specific activity (3,112.2 U/mg) than the wild type (2,047.3 U/mg). The Km decreased from 7.04 mM in the wild type to 5.19 mM in the mutant R157T, and the V max increased from 5.11 μM s-1 in the wild type to 7.56 μM s-1 in the mutant R157T.IMPORTANCE We successfully achieved efficient secretory production and improved the catalytic efficiency of diacetylchitobiose deacetylase in Bacillus subtilis, and this provides a good foundation for the application of diacetylchitobiose deacetylase in the production of chitosan oligosaccharides and monosaccharides.
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98
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Deng J, Chen C, Gu Y, Lv X, Liu Y, Li J, Ledesma-Amaro R, Du G, Liu L. Creating an in vivo bifunctional gene expression circuit through an aptamer-based regulatory mechanism for dynamic metabolic engineering in Bacillus subtilis. Metab Eng 2019; 55:179-190. [PMID: 31336181 DOI: 10.1016/j.ymben.2019.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 11/16/2022]
Abstract
Aptamer-based regulatory biosensors can dynamically regulate the expression of target genes in response to ligands and could be used in dynamic metabolic engineering for pathway optimization. However, the existing aptamer-ligand biosensors can only function with non-complementary DNA elements that cannot replicate in growing cells. Here, we construct an aptamer-based synthetic regulatory circuit that can dynamically upregulate and downregulate the expression of target genes in response to the ligand thrombin at transcriptional and translational levels, respectively, and further used this system to dynamically engineer the synthesis of 2'-fucosyllactose (2'-FL) in Bacillus subtilis. First, we demonstrated the binding of ligand molecule thrombin with the aptamer can induce the unwinding of fully complementary double-stranded DNA. Based on this finding, we constructed a bifunctional gene expression regulatory circuit using ligand thrombin-bound aptamers. The expression of the reporter gene ranged from 0.084- to 48.1-fold. Finally, by using the bifunctional regulatory circuit, we dynamically upregulated the expression of key genes fkp and futC and downregulated the expression of gene purR, resulting in the significant increase of 2'-FL titer from 24.7 to 674 mg/L. Compared with the other pathway-specific dynamic engineering systems, here the constructed aptamer-based regulatory circuit is independent of pathways, and can be generally used to fine-tune gene expression in other microbes.
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Affiliation(s)
- Jieying Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Chunmei Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yang Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | | | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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99
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Castillo-Hair SM, Fujita M, Igoshin OA, Tabor JJ. An Engineered B. subtilis Inducible Promoter System with over 10 000-Fold Dynamic Range. ACS Synth Biol 2019; 8:1673-1678. [PMID: 31181163 DOI: 10.1021/acssynbio.8b00469] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacillus subtilis is the leading model Gram-positive bacterium, and a widely used chassis for industrial protein production. However, B. subtilis research is limited by a lack of inducible promoter systems with low leakiness and high dynamic range. Here, we engineer an inducible promoter system based on the T7 RNA Polymerase (T7 RNAP), the lactose repressor LacI, and the chimeric promoter PT7lac, integrated as a single copy in the B. subtilis genome. In the absence of IPTG, LacI strongly represses T7 RNAP and PT7lac and minimizes leakiness. Addition of IPTG derepresses PT7lac and simultaneously induces expression of T7RNAP, which results in very high output expression. Using green fluorescent and β-galactosidase reporter proteins, we estimate that this LacI-T7 system can regulate expression with a dynamic range of over 10 000, by far the largest reported for an inducible B. subtilis promoter system. Furthermore, LacI-T7 responds to similar IPTG concentrations and with similar kinetics as the widely used Phy-spank IPTG-inducible system, which we show has a dynamic range of at most 300 in a similar genetic context. Due to its superior performance, our LacI-T7 system should have broad applications in fundamental B. subtilis biology studies and biotechnology.
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Affiliation(s)
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Road, Houston, Texas 77004, United States
| | - Oleg A. Igoshin
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Center for Theoretical Biophysics, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Jeffrey J. Tabor
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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100
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Wei R, Breite D, Song C, Gräsing D, Ploss T, Hille P, Schwerdtfeger R, Matysik J, Schulze A, Zimmermann W. Biocatalytic Degradation Efficiency of Postconsumer Polyethylene Terephthalate Packaging Determined by Their Polymer Microstructures. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900491. [PMID: 31380212 PMCID: PMC6662049 DOI: 10.1002/advs.201900491] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/24/2019] [Indexed: 05/09/2023]
Abstract
Polyethylene terephthalate (PET) is the most important mass-produced thermoplastic polyester used as a packaging material. Recently, thermophilic polyester hydrolases such as TfCut2 from Thermobifida fusca have emerged as promising biocatalysts for an eco-friendly PET recycling process. In this study, postconsumer PET food packaging containers are treated with TfCut2 and show weight losses of more than 50% after 96 h of incubation at 70 °C. Differential scanning calorimetry analysis indicates that the high linear degradation rates observed in the first 72 h of incubation is due to the high hydrolysis susceptibility of the mobile amorphous fraction (MAF) of PET. The physical aging process of PET occurring at 70 °C is shown to gradually convert MAF to polymer microstructures with limited accessibility to enzymatic hydrolysis. Analysis of the chain-length distribution of degraded PET by nuclear magnetic resonance spectroscopy reveals that MAF is rapidly hydrolyzed via a combinatorial exo- and endo-type degradation mechanism whereas the remaining PET microstructures are slowly degraded only by endo-type chain scission causing no detectable weight loss. Hence, efficient thermostable biocatalysts are required to overcome the competitive physical aging process for the complete degradation of postconsumer PET materials close to the glass transition temperature of PET.
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Affiliation(s)
- Ren Wei
- Department of Microbiology and Bioprocess TechnologyInstitute of BiochemistryLeipzig UniversityJohannisallee 23D‐04103LeipzigGermany
| | - Daniel Breite
- Leibniz Institute of Surface Engineering (IOM)Permoserstrasse 15D‐04318LeipzigGermany
| | - Chen Song
- Institute of Analytical ChemistryLeipzig UniversityLinnéstrasse 3D‐04103LeipzigGermany
| | - Daniel Gräsing
- Institute of Analytical ChemistryLeipzig UniversityLinnéstrasse 3D‐04103LeipzigGermany
| | - Tina Ploss
- AB Enzymes GmbHFeldbergstrasse 78D‐64293DarmstadtGermany
| | - Patrick Hille
- Department of Microbiology and Bioprocess TechnologyInstitute of BiochemistryLeipzig UniversityJohannisallee 23D‐04103LeipzigGermany
| | | | - Jörg Matysik
- Institute of Analytical ChemistryLeipzig UniversityLinnéstrasse 3D‐04103LeipzigGermany
| | - Agnes Schulze
- Leibniz Institute of Surface Engineering (IOM)Permoserstrasse 15D‐04318LeipzigGermany
| | - Wolfgang Zimmermann
- Department of Microbiology and Bioprocess TechnologyInstitute of BiochemistryLeipzig UniversityJohannisallee 23D‐04103LeipzigGermany
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