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Piri-Gharaghie T, Ghourchian H, Rezaeizadeh G, Kabiri H, Rajaei N, Dhiaa AM, Ghajari G, Bahari R. (S)-3-(3,4-Dihydroxybenzyl) piperazine-2,5-dione (cyclo-Gly-L-DOPA or CG-Nio-CGLD) peptide loaded in Chitosan Glutamate-Coated Niosomes as anti-Colorectal cancer activity. BMC Pharmacol Toxicol 2024; 25:44. [PMID: 39090674 DOI: 10.1186/s40360-024-00766-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 07/16/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC), now the second most prevalent malignant tumor worldwide, is more prevalent in young adults. In recent decades, there has been progress in creating anti-colorectal cancer medications, including cytotoxic compounds. OBJECTIVES Novel anticancer drugs are needed to surmount existing obstacles. A recent study investigated the effectiveness of novel formulations in preventing colorectal cancer. METHODS During this study, we assessed a new kind of niosome called cyclo-Gly-L-DOPA (CG-Nio-CGLD) made from chitosan glutamate. We evaluated the anti-colorectal cancer properties of CG-Nio-CGLD utilizing CCK-8, invasion assay, MTT assay, flow cytometry, and cell cycle analysis. The transcription of genes associated with apoptosis was analyzed using quantitative real-time PCR. At the same time, the cytotoxicity of nanomaterials on both cancer and normal cell lines was assessed using MTT assays. Novel anticancer drugs are needed to surmount existing obstacles. A recent study investigated the effectiveness of newly developed formulations in preventing colorectal cancer. RESULTS The Nio-CGLD and CG-Nio-CGLD were spherical mean diameters of 169.12 ± 1.87 and 179.26 ± 2.17 nm, respectively. Entrapment efficiency (EE%) measurements of the Nio-CGLD and CG-Nio-CGLD were 63.12 ± 0.51 and 76.43 ± 0.34%, respectively. In the CG-Nio-CGLD group, the percentages of early, late, necrotic, and viable CL40 cells were 341.93%, 23.27%, 9.32%, and 25.48%. The transcription of the genes PP53, cas3, and cas8 was noticeably higher in the treatment group compared to the control group (P > 0.001). Additionally, the treatment group had lower BCL2 and survivin gene expression levels than the control group (P < 0.01). Additionally, CG-Nio-CGLD formulations demonstrated a biocompatible nanoscale delivery mechanism and displayed little cytotoxicity toward the CCD 841 CoN reference cell line. CONCLUSION These findings indicate that chitosan-based noisome encapsulation may enhance the effectiveness of CG-Nio-CGLD formulations in fighting cancer.
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Affiliation(s)
- Tohid Piri-Gharaghie
- Biotechnology Research Center, Faculty of Biological Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Hedieh Ghourchian
- Department of Biology, Faculty of Biological Science, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Golnoosh Rezaeizadeh
- Department of Microbiology, Faculty of Biological Sciences, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
| | - Hamidreza Kabiri
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
- Sina Borna Aria (SABA) Co., Ltd, Research and Development Center for Biotechnology, Shahrekord, Iran
| | - Negin Rajaei
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
- Sina Borna Aria (SABA) Co., Ltd, Research and Development Center for Biotechnology, Shahrekord, Iran
| | | | - Ghazal Ghajari
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Roghayeh Bahari
- Department of Biology, Faculty of Biological Science, Urmia Branch, Islamic Azad University, Urmia, Iran
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Ma D, Chen H, Liu D, Feng C, Hua Y, Gu T, Guo X, Zhou Y, Wang H, Tong G, Li H, Zhang K. Soil-derived cellulose-degrading bacteria: screening, identification, the optimization of fermentation conditions, and their whole genome sequencing. Front Microbiol 2024; 15:1409697. [PMID: 39050626 PMCID: PMC11266136 DOI: 10.3389/fmicb.2024.1409697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Straw cellulose is an abundant renewable resource in nature. In recent years, the conversion of cellulose from waste straw into biofuel by specific microorganisms' fragmentation has attracted extensive attention. Although many bacteria with the ability to degrade cellulose have been identified, comprehensive bioinformatics analyses of these bacteria remain limited, and research exploring optimal fragmentation conditions is scarce. Our study involved the isolation and screening of bacteria from various locations in Yangzhou using carboxymethyl cellulose (CMC) media. Then, the cellulose-degrading bacteria were identified using 16S rRNA and seven candidate bacterial strains with cellulose degrading ability were identified in Yangzhou city for the first time. The cellulase activity was determined by the 3,5-dinitrosalicylic acid (DNS) method in different fragmentation conditions, and finally two bacteria strains with the strongest cellulose degradation ability were selected for whole genome sequencing analysis. Sequencing results revealed that the genome sizes of Rhodococcus wratislaviensis YZ02 and Pseudomonas Xanthosomatis YZ03 were 8.51 Mb and 6.66 Mb, containing 8,466 and 5,745 genes, respectively. A large number of cellulose degradation-related genes were identified and annotated using KEGG, GO and COG analyses. In addition, genomic CAZyme analysis indicated that both R. wratislaviensis YZ02 and P. Xanthosomatis YZ03 harbor a series of glycoside hydrolase family (GH) genes and other genes related to cellulose degradation. Our finding provides new options for the development of cellulose-degrading bacteria and a theoretical basis for improving the cellulose utilization of straw.
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Affiliation(s)
- Degao Ma
- Yangzhou Environmental Monitoring Center of Jiangsu Province, Yangzhou, China
| | - Haoyu Chen
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Duxuan Liu
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Chenwei Feng
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Yanhong Hua
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Tianxiao Gu
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Xiao Guo
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Yuchen Zhou
- Department of Pharmacy, Medical School of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Houjun Wang
- Yangzhou Environmental Monitoring Center of Jiangsu Province, Yangzhou, China
| | - Guifeng Tong
- Yangzhou Environmental Monitoring Center of Jiangsu Province, Yangzhou, China
| | - Hua Li
- College of Engineering, Nanjing Agricultural University, Nanjing, China
| | - Kun Zhang
- College of Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
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Zhang G, Feng S, Qin M, Sun J, Liu Y, Luo C, Lin M, Xu S, Liao M, Fan H, Liang Z. Influence of PepF peptidase and sporulation on microcin J25 production in Bacillus subtilis. Microbiol Spectr 2024; 12:e0374823. [PMID: 38780256 PMCID: PMC11218540 DOI: 10.1128/spectrum.03748-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024] Open
Abstract
The lasso peptide microcin J25 (MccJ25) possesses strong antibacterial properties and is considered a potential effective component of bacterial disease treatment drugs and safe food preservatives. Although MccJ25 can be heterologously expressed in Bacillus subtilis as we have previously reported, its regulation and accumulation are yet to be understood. Here, we investigated the expression level and stability of MccJ25 in B. subtilis strains with disruption in peptidase genes pepA, pepF, and pepT. Oligoendopeptidase F (PepF) was found to be involved in reduction of the production of MccJ25 by degradation of its precursor peptide. In the pepF mutant, the MccJ25 reached a concentration of 1.68 µM after a cultivation time exceeding 60 hours, while the wild-type strain exhibited a concentration of only 0.14 µM. Moreover, the production of MccJ25 in B. subtilis downregulated the genes associated with sporulation, and this may contribute to its accumulation. Finally, this study provides a strategy to improve the stability and production of MccJ25 in B. subtilis. IMPORTANCE MccJ25 displays significant antibacterial activity, a well-defined mode of action, exceptional safety, and remarkable stability. Hence, it presents itself as a compelling candidate for an optimal antibacterial or anti-endotoxin medication. The successful establishment of exogenous production of MccJ25 in Bacillus subtilis provides a strategy for reducing its production cost and diversifying its utilization. In this study, we have provided evidence indicating that both peptidase PepF and sporulation are significant factors that limit the expression of MccJ25 in B. subtilis. The ΔpepF and ΔsigF mutants of B. subtilis express MccJ25 with higher production yield and enhanced stability. To sum up, this study developed several better engineered strains of B. subtilis, which greatly reduced the consumption of MccJ25 during the nutrient depletion stage of the host strain, improved its production, and elucidated factors that may be involved in reducing MccJ25 accumulation in B. subtilis.
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Affiliation(s)
- Guangwen Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Saixiang Feng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
| | - Miaomiao Qin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Juan Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yutong Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Changqi Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Min Lin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Siqi Xu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Huiying Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
| | - Zhaoping Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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Ferrando J, Miñana-Galbis D, Picart P. The Construction of an Environmentally Friendly Super-Secreting Strain of Bacillus subtilis through Systematic Modulation of Its Secretory Pathway Using the CRISPR-Cas9 System. Int J Mol Sci 2024; 25:6957. [PMID: 39000067 PMCID: PMC11240994 DOI: 10.3390/ijms25136957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
Achieving commercially significant yields of recombinant proteins in Bacillus subtilis requires the optimization of its protein production pathway, including transcription, translation, folding, and secretion. Therefore, in this study, our aim was to maximize the secretion of a reporter α-amylase by overcoming potential bottlenecks within the secretion process one by one, using a clustered regularly interspaced short palindromic repeat-Cas9 (CRISPR-Cas9) system. The strength of single and tandem promoters was evaluated by measuring the relative α-amylase activity of AmyQ integrated into the B. subtilis chromosome. Once a suitable promoter was selected, the expression levels of amyQ were upregulated through the iterative integration of up to six gene copies, thus boosting the α-amylase activity 20.9-fold in comparison with the strain harboring a single amyQ gene copy. Next, α-amylase secretion was further improved to a 26.4-fold increase through the overexpression of the extracellular chaperone PrsA and the signal peptide peptidase SppA. When the final expression strain was cultivated in a 3 L fermentor for 90 h, the AmyQ production was enhanced 57.9-fold. The proposed strategy allows for the development of robust marker-free plasmid-less super-secreting B. subtilis strains with industrial relevance.
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Affiliation(s)
| | | | - Pere Picart
- Faculty of Pharmacy and Food Science Technology, Department of Biology, Healthcare and the Environment, Microbiology Section, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; (J.F.); (D.M.-G.)
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Li K, Guo Y, Sun X, Xi X, Wang L, Ren X, Wang C, Liu X. Whole-cell biocatalysis for ε-poly-l-lysine production by a food-grade recombinant Bacillus subtilis. Enzyme Microb Technol 2024; 179:110467. [PMID: 38852284 DOI: 10.1016/j.enzmictec.2024.110467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 05/11/2024] [Accepted: 06/01/2024] [Indexed: 06/11/2024]
Abstract
ε-Poly-l-lysine (ε-PL), a natural food preservative with various advantages, is primarily produced by Streptomyces. It has attracted considerable attentions for the outstanding antibacterial activity, safety, heat stability, water solubility and other remarkable properties. In this study, a food-grade recombinant Bacillus subtilis was constructed for the biocatalysis of ε-PL. Firstly, the d-alanine racemase gene (alrA) was deleted from the genome of Bacillus subtilis 168 to construct an auxotrophic B. subtilis 168 (alrA-). Based on the shuttle plasmid pMA5, a food-grade plasmid pMA5a was constructed by replacing the genes of kanamycin resistance (Kanr) and ampicillin resistance (Ampr) with alrA and the gene encoding α-peptide of β-galactosidase (lacZα), respectively. Subsequently, codon-optimized ε-PL synthase gene (pls) and P-pls were ligated into pMA5a and transformed in E. coli DH5α and expressed in B. subtilis 168 (alrA-). Finally, the whole-cell biocatalysis conditions for ε-PL production by B. subtilis 168 (alrA-)/pMA5a-pls were optimized, and the optimal conditions were 30°C, pH 4, l-lysine concentration of 0.6 g/L, bacterial concentration of 15 % (w/v) and a catalytic time of 7 h. The ε-PL production reached a maximum of 0.33 ± 0.03 g/L. The product was verified to be ε-PL by HPLC and tricine-SDS-PAGE. The information obtained in this study shows critical reference for the food-grade heterologous expression of ε-PL.
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Affiliation(s)
- Kunpeng Li
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Yangzi Guo
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Xinjie Sun
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Xiangheng Xi
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Li Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Xidong Ren
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China.
| | - Chenying Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China.
| | - Xinli Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
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6
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Charoenwongpaiboon T, Charoenwongphaibun C, Wangpaiboon K, Panpetch P, Wanichacheva N, Pichyangkura R. Endo- and exo-levanases from Bacillus subtilis HM7: Catalytic components, synergistic cooperation, and application in fructooligosaccharide synthesis. Int J Biol Macromol 2024; 271:132508. [PMID: 38782321 DOI: 10.1016/j.ijbiomac.2024.132508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/28/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Levan-type fructooligosaccharides (LFOS) exhibit significant biological activities and selectively promote the growth of certain beneficial bacteria. Levanase is an important enzyme for LFOS production. In this study, two isoforms of levanases, exo- and endo-type depolymerizing enzymes, from Bacillus subtilis HM7 isolated from Dynastes hercules larvae excrement were cloned, expressed, and characterized. The synergistic effect on the levan hydrolysis and kinetic properties of both isoforms were evaluated, indicating their cooperation in levan metabolism, where the endo-levanase catalyzes a rate-limiting step. In addition, homology models and molecular dynamics simulations revealed the key amino residues of the enzymes for levan binding and catalysis. It was found that both isoforms possessed distinct binding residues in the active sites, suggesting the importance of the specificity of the enzymes. Finally, we demonstrated the potential of endo-type levanase in LFOS synthesis using a one-pot reaction with levansucrase. Overall, this study fills the knowledge gap in understanding levanase's mechanism, making an important contribution to the fields of food science and biotechnology.
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Affiliation(s)
| | - Chonnipha Charoenwongphaibun
- Division of Chemistry, Department of Physical and Material Sciences, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Sean, Nakhon Pathom 73140, Thailand
| | - Karan Wangpaiboon
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pawinee Panpetch
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nantanit Wanichacheva
- Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom 73000, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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Kamboj A, Dumka S, Saxena MK, Singh Y, Kaur BP, da Silva SJR, Kumar S. A Comprehensive Review of Our Understanding and Challenges of Viral Vaccines against Swine Pathogens. Viruses 2024; 16:833. [PMID: 38932126 PMCID: PMC11209531 DOI: 10.3390/v16060833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Pig farming has become a strategically significant and economically important industry across the globe. It is also a potentially vulnerable sector due to challenges posed by transboundary diseases in which viral infections are at the forefront. Among the porcine viral diseases, African swine fever, classical swine fever, foot and mouth disease, porcine reproductive and respiratory syndrome, pseudorabies, swine influenza, and transmissible gastroenteritis are some of the diseases that cause substantial economic losses in the pig industry. It is a well-established fact that vaccination is undoubtedly the most effective strategy to control viral infections in animals. From the period of Jenner and Pasteur to the recent new-generation technology era, the development of vaccines has contributed significantly to reducing the burden of viral infections on animals and humans. Inactivated and modified live viral vaccines provide partial protection against key pathogens. However, there is a need to improve these vaccines to address emerging infections more comprehensively and ensure their safety. The recent reports on new-generation vaccines against swine viruses like DNA, viral-vector-based replicon, chimeric, peptide, plant-made, virus-like particle, and nanoparticle-based vaccines are very encouraging. The current review gathers comprehensive information on the available vaccines and the future perspectives on porcine viral vaccines.
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Affiliation(s)
- Aman Kamboj
- College of Veterinary and Animal Sciences, G. B. Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India; (A.K.); (M.K.S.); (Y.S.)
| | - Shaurya Dumka
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati 781039, Assam, India; (S.D.); (B.P.K.)
| | - Mumtesh Kumar Saxena
- College of Veterinary and Animal Sciences, G. B. Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India; (A.K.); (M.K.S.); (Y.S.)
| | - Yashpal Singh
- College of Veterinary and Animal Sciences, G. B. Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India; (A.K.); (M.K.S.); (Y.S.)
| | - Bani Preet Kaur
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati 781039, Assam, India; (S.D.); (B.P.K.)
| | | | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati 781039, Assam, India; (S.D.); (B.P.K.)
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Chen Y, Li M, Yan M, Chen Y, Saeed M, Ni Z, Fang Z, Chen H. Bacillus subtilis: current and future modification strategies as a protein secreting factory. World J Microbiol Biotechnol 2024; 40:195. [PMID: 38722426 DOI: 10.1007/s11274-024-03997-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Bacillus subtilis is regarded as a promising microbial expression system in bioengineering due to its high stress resistance, nontoxic, low codon preference and grow fast. The strain has a relatively efficient expression system, as it has at least three protein secretion pathways and abundant molecular chaperones, which guarantee its expression ability and compatibility. Currently, many proteins are expressed in Bacillus subtilis, and their application prospects are broad. Although Bacillus subtilis has great advantages compared with other prokaryotes related to protein expression and secretion, it still faces deficiencies, such as low wild-type expression, low product activity, and easy gene loss, which limit its large-scale application. Over the years, many researchers have achieved abundant results in the modification of Bacillus subtilis expression systems, especially the optimization of promoters, expression vectors, signal peptides, transport pathways and molecular chaperones. An optimal vector with a suitable promoter strength and other regulatory elements could increase protein synthesis and secretion, increasing industrial profits. This review highlights the research status of optimization strategies related to the expression system of Bacillus subtilis. Moreover, research progress on its application as a food-grade expression system is also presented, along with some future modification and application directions.
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Affiliation(s)
- Yanzhen Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Miaomiao Li
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Mingchen Yan
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yong Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Muhammad Saeed
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zhong Ni
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zhen Fang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Huayou Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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Liu X, Lian M, Zhao M, Huang M. Advances in recombinant protease production: current state and perspectives. World J Microbiol Biotechnol 2024; 40:144. [PMID: 38532149 DOI: 10.1007/s11274-024-03957-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
Proteases, enzymes that catalyze the hydrolysis of peptide bonds in proteins, are important in the food industry, biotechnology, and medical fields. With increasing demand for proteases, there is a growing emphasis on enhancing their expression and production through microbial systems. However, proteases' native hosts often fall short in high-level expression and compatibility with downstream applications. As a result, the recombinant production of proteases has become a significant focus, offering a solution to these challenges. This review presents an overview of the current state of protease production in prokaryotic and eukaryotic expression systems, highlighting key findings and trends. In prokaryotic systems, the Bacillus spp. is the predominant host for proteinase expression. Yeasts are commonly used in eukaryotic systems. Recent advancements in protease engineering over the past five years, including rational design and directed evolution, are also highlighted. By exploring the progress in both expression systems and engineering techniques, this review provides a detailed understanding of the current landscape of recombinant protease research and its prospects for future advancements.
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Affiliation(s)
- Xiufang Liu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou, 510650, China
| | - Mulin Lian
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou, 510650, China
| | - Mouming Zhao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou, 510650, China
| | - Mingtao Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China.
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou, 510650, China.
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Das S, Chowdhury C, Kumar SP, Roy D, Gosavi SW, Sen R. Microbial production of N-acetyl-D-glucosamine (GlcNAc) for versatile applications: Biotechnological strategies for green process development. Carbohydr Res 2024; 536:109039. [PMID: 38277719 DOI: 10.1016/j.carres.2024.109039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 12/07/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024]
Abstract
N-acetyl-d-glucosamine (GlcNAc) is a commercially important amino sugar for its wide range of applications in pharmaceutical, food, cosmetics and biofuel industries. In nature, GlcNAc is polymerised into chitin biopolymer, which is one of the major constituents of fungal cell wall and outer shells of crustaceans. Sea food processing industries generate a large volume of chitin as biopolymeric waste. Because of its high abundance, chitinaceous shellfish wastes have been exploited as one of the major precursor substrates of GlcNAc production, both in chemical and enzymatic means. Nevertheless, the current process of GlcNAc extraction from shellfish wastes generates poor turnover and attracts environmental hazards. Moreover, GlcNAc isolated from shellfish could not be prescribed to certain groups of people because of the allergic nature of shell components. Therefore, an alternative route of GlcNAc production is advocated. With the advancement of metabolic construction and synthetic biology, microbial synthesis of GlcNAc is gaining much attention nowadays. Several new and cutting-edge technologies like substrate co-utilization strategy, promoter engineering, and CRISPR interference system were proposed in this fascinating area. The study would put forward the potential application of microbial engineering in the production of important pharmaceuticals. Very recently, autotrophic fermentation of GlcNAc synthesis has been proposed. The metabolic engineering approaches would offer great promise to mitigate the issues of low yield and high production cost, which are major challenges in microbial bio-processes industries. Further process optimization, optimising metabolic flux, and efficient recovery of GlcNAc from culture broth, should be investigated in order to achieve a high product titer. The current study presents a comprehensive review on microbe-based eco-friendly green methods that would pave the way towards the development of future research directions in this field for the designing of a cost-effective fermentation process on an industrial setup.
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Affiliation(s)
- Sancharini Das
- Department of Environmental Science, Savitribai Phule Pune University, Pune, MH, 411007, India; Department of Biotechnology, Indian Institute of Technology Kharagpur, WB, 721302, India.
| | - Chiranjit Chowdhury
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, MH, 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - S Pavan Kumar
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, TN, 600 036, India
| | - Debasis Roy
- Department of Civil Engineering, Indian Institute of Technology Kharagpur, WB, 721302, India
| | - Suresh W Gosavi
- Department of Environmental Science, Savitribai Phule Pune University, Pune, MH, 411007, India
| | - Ramkrishna Sen
- Department of Biotechnology, Indian Institute of Technology Kharagpur, WB, 721302, India
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11
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Yan C, Ji S, Wu R, Li M, He K, Shi H, Wang C, Yang H, Guo J, Wu J. Structural properties and biological activities of the extracellular polysaccharide of Bacillus subtilis LZ13-4. Int J Biol Macromol 2024; 259:129176. [PMID: 38181904 DOI: 10.1016/j.ijbiomac.2023.129176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 12/18/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024]
Abstract
The remarkable functional characteristics of Bacillus subtilis extracellular polysaccharides (BSPS) are of great interest. Therefore, in the present study, BSPS was isolated and characterized to obtain two fractions, BSPS-1 and BSPS-2, respectively, and to investigate their biological activities. BSPS-1 contained fructose, glucose, and galactose (molar ratio: 25.27:43.37:31.36), while BSPS-2 contained fructose with only trace amounts of glucose, galactose, and mannose (molar ratio: 55.08:19.03:19.21:6.68), and their respective average molecular weights were 16.9 kDa and 202.67 kDa. With a 93.55 % clearance of ABTS•+ at a concentration of 2 mg/mL of BSPS-1, the antioxidant activity revealed that BSPS-1 had greater antioxidant activity than BSPS-2 and that both were concentration-dependent. The inhibitory effect on HepG2 cells demonstrated that BSPS-1 and BSPS-2 significantly inhibited the proliferation of HepG2 and increased the expression of apoptotic proteins, causing apoptosis. The inhibition rate on HepG2 cells was dose-dependent and reached 52.7 % and 40.3 % after 48 h of action. BSPS-2 and 800 μg/mL BSPS-1 growth was inhibited in the G1/G0 phase, while 200 and 400 μg/mL BSPS-1 growth was inhibited in the S phase. In conclusion, the study of the BSPS's structure and properties can offer a theoretical foundation for real-world industrial applications.
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Affiliation(s)
- Chunyue Yan
- College of Food Science, Shenyang Agricultural University, Engineering Research Center of Food Fermentation Technology, Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, Liaoning 110866, P.R. China
| | - Shuaiqi Ji
- College of Food Science, Shenyang Agricultural University, Engineering Research Center of Food Fermentation Technology, Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, Liaoning 110866, P.R. China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Engineering Research Center of Food Fermentation Technology, Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, Liaoning 110866, P.R. China
| | - Mo Li
- College of Criminal Science and Technology, Criminal Investigation Police University of China, Shenyang, Liaoning, 110854, P.R. China
| | - Kairu He
- College of Food Science, Shenyang Agricultural University, Engineering Research Center of Food Fermentation Technology, Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, Liaoning 110866, P.R. China
| | - Haisu Shi
- College of Food Science, Shenyang Agricultural University, Engineering Research Center of Food Fermentation Technology, Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, Liaoning 110866, P.R. China
| | - Cong Wang
- College of Food Science, Shenyang Agricultural University, Engineering Research Center of Food Fermentation Technology, Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, Liaoning 110866, P.R. China
| | - Hui Yang
- College of Food Science, Shenyang Agricultural University, Engineering Research Center of Food Fermentation Technology, Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, Liaoning 110866, P.R. China
| | - Jia Guo
- College of Food Science, Shenyang Agricultural University, Engineering Research Center of Food Fermentation Technology, Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, Liaoning 110866, P.R. China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Engineering Research Center of Food Fermentation Technology, Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, Liaoning 110866, P.R. China.
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12
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Wang B, van der Kloet F, Hamoen LW. Induction of the CtsR regulon improves Xylanase production in Bacillus subtilis. Microb Cell Fact 2023; 22:231. [PMID: 37946188 PMCID: PMC10633939 DOI: 10.1186/s12934-023-02239-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The bacterium Bacillus subtilis is extensively used for the commercial production of enzymes due to its efficient protein secretion capacity. However, the efficiency of secretion varies greatly between enzymes, and despite many years of research, optimization of enzyme production is still largely a matter of trial-and-error. Genome-wide transcriptome analysis seems a useful tool to identify relevant secretion bottlenecks, yet to this day, only a limited number of transcriptome studies have been published that focus on enzyme secretion in B. subtilis. Here, we examined the effect of high-level expression of the commercially important enzyme endo-1,4-β-xylanase XynA on the B. subtilis transcriptome using RNA-seq. RESULTS Using the novel gene-set analysis tool GINtool, we found a reduced activity of the CtsR regulon when XynA was overproduced. This regulon comprises several protein chaperone genes, including clpC, clpE and clpX, and is controlled by transcriptional repression. CtsR levels are directly controlled by regulated proteolysis, involving ClpC and its cognate protease ClpP. When we abolished this negative feedback, by inactivating the repressor CtsR, the XynA production increased by 25%. CONCLUSIONS Overproduction of enzymes can reduce the pool of Clp protein chaperones in B. subtilis, presumably due to negative feedback regulation. Breaking this feedback can improve enzyme production yields. Considering the conserved nature of Clp chaperones and their regulation, this method might benefit high-yield enzyme production in other organisms.
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Affiliation(s)
- Biwen Wang
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, C3.108, 1098 XH, Amsterdam, The Netherlands
| | - Frans van der Kloet
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, C3.108, 1098 XH, Amsterdam, The Netherlands
| | - Leendert W Hamoen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, C3.108, 1098 XH, Amsterdam, The Netherlands.
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13
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Wahjudi SMW, Petrzik T, Oudenne F, Lera Calvo C, Büchs J. Unraveling the potential and constraints associated with corn steep liquor as a nutrient source for industrial fermentations. Biotechnol Prog 2023; 39:e3386. [PMID: 37634939 DOI: 10.1002/btpr.3386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023]
Abstract
Costly complex media components such as yeast extract and peptone are still widely used in industrial bioprocesses, despite their ill-defined composition. Side stream products such as corn steep liquor (CSL) present a compelling economical alternative that contains valuable nutrients required for microbial growth, that is, nitrogen and amino acids, but also vitamins, trace elements, and other minerals. However, as a side stream product, CSL may be subject to batch-to-batch variations and compositional heterogeneity. In this study, the Respiration Activity MOnitoring System designed for shake flasks (RAMOS) and 96-well microtiter plates (μTOM) were applied to investigate the potential and constraints of CSL utilization for two model microorganisms: E. coli and B. subtilis. Considering the dry substance content of complex nutrients involved, CSL-based media are more efficient in biomass production than the common lysogeny broth (LB) medium, containing 5 g/L yeast extract, 10 g/L peptone, and 5 g/L NaCl. At a glucose to CSL (glucose/CSL, g/g) ratio of 1/1 (g/g) and 2/1 (g/g), a secondary substrate limitation occurred in E. coli and B. subtilis cultivations, respectively. The study sheds light on differences in the metabolic activity of the two applied model organisms between varying CSL batches, which relate to CSL origin and production process, as well as the effect of targeted nutrient supplementation. Through a targeted nutrient supplementation, the most limiting component of the CSL-glucose medium used for these applied model microorganisms was identified to be ammonium nitrogen. This study proves the suitability of CSL as an alternative nutrient source for E. coli and B. subtilis. The RAMOS and μTOM technique detected differences between CSL batches, allowing easy and early identification of varying batches. A consistent performance of the CSL batches in E. coli and B. subtilis cultivations was demonstrated.
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Affiliation(s)
| | - Thomas Petrzik
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | | | | | - Jochen Büchs
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
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14
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Zhao R, Chen Z, Liang J, Dou J, Guo F, Xu Z, Wang T. Advances in Genetic Tools and Their Application in Streptococcus thermophilus. Foods 2023; 12:3119. [PMID: 37628118 PMCID: PMC10453384 DOI: 10.3390/foods12163119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/13/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Streptococcus thermophilus is a traditional starter. Nowadays, key aspects of S. thermophilus physiology have been revealed concerning the phenotypic traits relevant for industrial applications, including sugar metabolism, protein hydrolysis, and the production of important metabolites that affect the sensory properties of fermented foods as well as the original cooperation with Lactobacillus delbrueckii subsp. bulgaricus. Moreover, significant advances have been made in the synthetic biology toolbox of S. thermophilus based on technological advances in the genome and its sequencing and synthesis. In this review, we discuss the recently developed toolbox for S. thermophilus, including gene expression toolsets (promoters, terminators, plasmids, etc.) and genome editing tools. It can be used for both functionalized foods and therapeutic molecules for consumers. The availability of new molecular tools, including the genome editing toolbox, has facilitated the engineering of physiological studies of S. thermophilus and the generation of strains with improved technical and functional characteristics.
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Affiliation(s)
- Ruiting Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China; (R.Z.); (Z.C.); (J.L.); (J.D.); (F.G.); (T.W.)
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Zouquan Chen
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China; (R.Z.); (Z.C.); (J.L.); (J.D.); (F.G.); (T.W.)
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Jie Liang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China; (R.Z.); (Z.C.); (J.L.); (J.D.); (F.G.); (T.W.)
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Jiaxin Dou
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China; (R.Z.); (Z.C.); (J.L.); (J.D.); (F.G.); (T.W.)
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Fangyu Guo
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China; (R.Z.); (Z.C.); (J.L.); (J.D.); (F.G.); (T.W.)
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Zhenshang Xu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China; (R.Z.); (Z.C.); (J.L.); (J.D.); (F.G.); (T.W.)
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Ting Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China; (R.Z.); (Z.C.); (J.L.); (J.D.); (F.G.); (T.W.)
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
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15
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Zhang G, Lin M, Qin M, Xie Q, Liang M, Jiang J, Dai H, Xu S, Feng S, Liao M. Establishing Heterologous Production of Microcins J25 and Y in Bacillus subtilis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5600-5613. [PMID: 36995900 DOI: 10.1021/acs.jafc.3c00675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Microcin J25 (MccJ25) and microcin Y (MccY) are lasso peptides and considered potential alternatives to antibiotics and harmful preservatives. The combination of these two microcins can provide a wide antimicrobial spectrum against food-borne Salmonella. Currently, MccJ25 and MccY are produced using Escherichia coli expression systems; however, the entire production process is accompanied by negative effects from endotoxins. In this study, we identified Bacillus subtilis as a suitable host for MccJ25 and MccY production. High-level production of microcins was achieved by promoter optimization, host strain selection, and recombinant expression. The engineered strains produced maximum yields of 2.827 μM MccJ25 and 1.481 μM MccY. This is the first study to demonstrate the expression of MccJ25 and MccY in B. subtilis, and it offers a few engineered strains that are without antibiotic resistance markers, inducer-free, sporulation-deficient, and free of the negative effects of endotoxins for antibacterial therapy and food preservation.
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Affiliation(s)
- Guangwen Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Min Lin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Miaomiao Qin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Qianmei Xie
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Mingzhi Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Jinfei Jiang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Huilin Dai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Siqi Xu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Saixiang Feng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, P. R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, P. R. China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Guangzhou 510642, P. R. China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou 510642, P. R. China
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, P. R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, P. R. China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Guangzhou 510642, P. R. China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou 510642, P. R. China
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16
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Wang S, Zhao Y, Mao S, Zhu J, Zhan Y, Cai D, Ma X, Wang D, Chen S. Enhancing the activity of disulfide-bond-containing proteins via promoting disulfide bond formation in Bacillus licheniformis. Int J Biol Macromol 2023; 233:123468. [PMID: 36731702 DOI: 10.1016/j.ijbiomac.2023.123468] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/01/2023]
Abstract
Disulfide bonds in proteins have strongly influence on the folding efficiency by constraining the conformational space. The inefficient disulfide bond formation of proteins is the main limiting factor of enzyme activity and stability. This study aimed to increase the activity of disulfide-bond-containing proteins via promoting disulfide bonds formation in Bacillus licheniformis. Initially, the glutamate decarboxylase GAD from Escherichia coli was selected as the model protein and introduced into the B. licheniformis. Then, the disulfide isomerase and oxidoreductase from different sources were excavated and overexpressed successively to improve the catalytic efficiency of GAD. The final engineered B. licheniformis showed significantly improved GAD specific activity (from 10.4 U/mg to 80.0 U/mg), which also presented perfect adaptability for other disulfide-bond-containing proteins, for instance, UDP-glucosyltransferase from Arabidopsis thaliana. Taken together, our work demonstrated that the activity of GAD in B. licheniformis was regulated by the disulfide bonds formation status and provided a promising platform for the expression of disulfide-bond-containing proteins.
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Affiliation(s)
- Shiyi Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yiwen Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Shufen Mao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Jiang Zhu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yangyang Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Xin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Dong Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China.
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China.
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17
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Calvanese M, Balestra C, Colarusso A, Lauro C, Riccardi C, Fondi M, Parrilli E, Tutino ML. Development of high-copy number plasmids in Pseudoalteromonas haloplanktis TAC125. Appl Microbiol Biotechnol 2023; 107:2469-2481. [PMID: 36912903 PMCID: PMC10033558 DOI: 10.1007/s00253-023-12448-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/23/2023] [Accepted: 02/21/2023] [Indexed: 03/14/2023]
Abstract
The Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) is considered an interesting alternative host for the recombinant protein production, that can be explored when the conventional bacterial expression systems fail. Indeed, the manufacture of all the difficult-to-express proteins produced so far in this bacterial platform gave back soluble and active products. Despite these promising results, the low yield of recombinant protein production achieved is hampering the wider and industrial exploitation of this psychrophilic cell factory. All the expression plasmids developed so far in PhTAC125 are based on the origin of replication of the endogenous pMtBL plasmid and are maintained at a very low copy number. In this work, we set up an experimental strategy to select mutated OriR sequences endowed with the ability to establish recombinant plasmids at higher multiplicity per cell. The solution to this major production bottleneck was achieved by the construction of a library of psychrophilic vectors, each containing a randomly mutated version of pMtBL OriR, and its screening by fluorescence-activated cell sorting (FACS). The selected clones allowed the identification of mutated OriR sequences effective in enhancing the plasmid copy number of approximately two orders of magnitude, and the production of the recombinant green fluorescent protein was increased up to twenty times approximately. Moreover, the molecular characterization of the different mutant OriR sequences allowed us to suggest some preliminary clues on the pMtBL replication mechanism that deserve to be further investigated in the future. KEY POINTS: • Setup of an electroporation procedure for Pseudoalteromonas haloplanktis TAC125. • Two order of magnitude improvement of OriR-derived psychrophilic expression systems. • Almost twenty times enhancement in Green fluorescent protein production.
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Affiliation(s)
- Marzia Calvanese
- Department of Chemical Sciences, Federico II University of Naples, Complesso Universitario Monte S.- Angelo, Via Cintia, 80126, Naples, Italy
| | - Cecilia Balestra
- Istituto Nazionale di Oceanografia e di Geofisica Sperimentale, Oceanography Division - OGS, Trieste, Italy
| | - Andrea Colarusso
- Department of Chemical Sciences, Federico II University of Naples, Complesso Universitario Monte S.- Angelo, Via Cintia, 80126, Naples, Italy
- Istituto Nazionale Biostrutture e Biosistemi I.N.B.B, Viale Medaglie d'Oro, 305-00136, Rome, Italy
| | - Concetta Lauro
- Department of Chemical Sciences, Federico II University of Naples, Complesso Universitario Monte S.- Angelo, Via Cintia, 80126, Naples, Italy
- Istituto Nazionale Biostrutture e Biosistemi I.N.B.B, Viale Medaglie d'Oro, 305-00136, Rome, Italy
| | - Christopher Riccardi
- Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, 50018, Florence, Italy
| | - Marco Fondi
- Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, 50018, Florence, Italy
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, Federico II University of Naples, Complesso Universitario Monte S.- Angelo, Via Cintia, 80126, Naples, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, Federico II University of Naples, Complesso Universitario Monte S.- Angelo, Via Cintia, 80126, Naples, Italy.
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18
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Nakharuthai C, Boonanuntanasarn S, Kaewda J, Manassila P. Isolation of Potential Probiotic Bacillus spp. from the Intestine of Nile Tilapia to Construct Recombinant Probiotic Expressing CC Chemokine and Its Effectiveness on Innate Immune Responses in Nile Tilapia. Animals (Basel) 2023; 13:986. [PMID: 36978530 PMCID: PMC10044694 DOI: 10.3390/ani13060986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
This study aimed to investigate the potential probiotic Bacillus spp. from the intestine of Nile tilapia in order to construct a recombinant probiotic for the enhancement of the Nile tilapia immune response. One hundred bacterial isolates from the intestine of Nile tilapia were characterized for species identification using the 16s ribosomal RNA (rRNA). Only Bacillus isolates with exhibited antagonistic activity were investigated for their biological functions, which included protease-producing capacity, bile salts and pH tolerance, antibiotic susceptibility, and pathogenicity tests. According to the best results, Bacillus isolate B29, as closely related to B. subtilis, was selected to construct a recombinant probiotic for the delivery of CC chemokine protein (pBESOn-CC). The existence of recombinant probiotics was confirmed by Western blotting before the feeding trial. In addition, the CC chemokine mRNA level was quantified in the intestine of fish fed probiotics after 30 days of feeding. Total immunoglobulin, lysozyme activity, alternative complement 50 activity (ACH50), and phagocytic activity of fish fed either wild-type or recombinant probiotics were significantly increased, indicating that probiotics could stimulate the Nile tilapia immune system through different processes. Interestingly, the dietary supplementation of recombinant probiotics has a stronger immune response enhancement than the wild-type strain.
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Affiliation(s)
- Chatsirin Nakharuthai
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Muang, Nakhon Ratchasima 30000, Thailand
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Naveed M, Wang Y, Yin X, Chan MWH, Aslam S, Wang F, Xu B, Ullah A. Purification, Characterization and Bactericidal Action of Lysozyme, Isolated from Bacillus subtillis BSN314: A Disintegrating Effect of Lysozyme on Gram-Positive and Gram-Negative Bacteria. Molecules 2023; 28:molecules28031058. [PMID: 36770725 PMCID: PMC9919333 DOI: 10.3390/molecules28031058] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
In the present study, lysozyme was purified by the following multi-step methodology: salt (ammonium sulfate) precipitation, dialysis, and ultrafiltration. The lysozyme potential was measured by enzymatic activity after each purification step. However, after ultrafiltration, the resulting material was considered extra purified. It was concentrated in an ultrafiltration centrifuge tube, and the resulting protein/lysozyme was used to determine its bactericidal potential against five bacterial strains, including three gram-positive (Bacillus subtilis 168, Micrococcus luteus, and Bacillus cereus) and two gram-negative (Salmonella typhimurium and Pseudomonas aeruginosa) strains. The results of ZOI and MIC/MBC showed that lysozyme had a higher antimicrobial activity against gram-positive than gram-negative bacterial strains. The results of the antibacterial activity of lysozyme were compared with those of ciprofloxacin (antibiotic). For this purpose, two indices were applied in the present study: antimicrobial index (AMI) and percent activity index (PAI). It was found that the purified lysozyme had a higher antibacterial activity against Bacillus cereus (AMI/PAI; 1.01/101) and Bacillus subtilis 168 (AMI/PAI; 1.03/103), compared to the antibiotic (ciprofloxacin) used in this study. Atomic force microscopy (AFM) was used to determine the bactericidal action of the lysozyme on the bacterial cell. The purified protein was further processed by gel column chromatography and the eluate was collected, its enzymatic activity was 21.93 U/mL, while the eluate was processed by native-PAGE. By this analysis, the un-denatured protein with enzymatic activity of 40.9 U/mL was obtained. This step shows that the protein (lysozyme) has an even higher enzymatic potential. To determine the specific peptides (in lysozyme) that may cause the bactericidal potential and cell lytic/enzymatic activity, the isolated protein (lysozyme) was further processed by the SDS-PAGE technique. SDS-PAGE analysis revealed different bands with sizes of 34 kDa, 24 kDa, and 10 kDa, respectively. To determine the chemical composition of the peptides, the bands (from SDS-PAGE) were cut, enzymatically digested, desalted, and analyzed by LC-MS (liquid chromatography-mass spectrometry). LC-MS analysis showed that the purified lysozyme had the following composition: the number of proteins in the sample was 56, the number of peptides was 124, and the number of PSMs (peptide spectrum matches) was 309. Among them, two peptides related to lysozyme and bactericidal activities were identified as: A0A1Q9G213 (N-acetylmuramoyl-L-alanine amidase) and A0A1Q9FRD3 (D-alanyl-D-alanine carboxypeptidase). The corresponding protein sequence and nucleic acid sequence were determined by comparison with the database.
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Affiliation(s)
- Muhammad Naveed
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
- School of Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Yadong Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
- School of Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Xian Yin
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
- School of Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Malik Wajid Hussain Chan
- Department of Chemistry, Faculty of Science, Federal Urdu University of Arts, Science and Technology, Campus Gulshan-e-Iqbal, Karachi 75300, Pakistan
| | - Sadar Aslam
- Department of Biological Science, University of Baltistan, Skardu 16400, Pakistan
| | - Fenghuan Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
- School of Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Correspondence: (F.W.); (B.X.)
| | - Baocai Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
- School of Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Correspondence: (F.W.); (B.X.)
| | - Asad Ullah
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
- School of Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Food and Marine Resources Research Center, Pakistan Council of Scientific and Industrial Research Laboratories Complex, Karachi 75280, Pakistan
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Lavania S, Choudhury B. Improvement of amidase production with high specific acyltransferase activity using Bacillus smithii IITR6B2. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Harirchi S, Sar T, Ramezani M, Aliyu H, Etemadifar Z, Nojoumi SA, Yazdian F, Awasthi MK, Taherzadeh MJ. Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives. Microorganisms 2022; 10:microorganisms10122355. [PMID: 36557608 PMCID: PMC9781867 DOI: 10.3390/microorganisms10122355] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.
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Affiliation(s)
- Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Taner Sar
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Mohaddaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Habibu Aliyu
- Institute of Process Engineering in Life Science II: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Zahra Etemadifar
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan 8174673441, Iran
| | - Seyed Ali Nojoumi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439957131, Iran
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Xianyang 712100, China
| | - Mohammad J. Taherzadeh
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
- Correspondence:
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Research Progress on the Effect of Autolysis to Bacillus subtilis Fermentation Bioprocess. FERMENTATION 2022. [DOI: 10.3390/fermentation8120685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacillus subtilis is a gram-positive bacterium, a promising microorganism due to its strong extracellular protein secretion ability, non-toxic, and relatively mature industrial fermentation technology. However, cell autolysis during fermentation restricts the industrial application of B. subtilis. With the fast advancement of molecular biology and genetic engineering technology, various advanced procedures and gene editing tools have been used to successfully construct autolysis-resistant B. subtilis chassis cells to manufacture various biological products. This paper first analyses the causes of autolysis in B. subtilis from a mechanistic perspective and outlines various strategies to address autolysis in B. subtilis. Finally, potential strategies for solving the autolysis problem of B. subtilis are foreseen.
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Zhang W, Wei M, Sun X, Lu F, Guan L, Mao S, Qin HM. Fine-Tuning of Carbon Flux and Artificial Promoters in Bacillus subtilis Enables High-Level Biosynthesis of d-Allulose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:13935-13944. [PMID: 36278912 DOI: 10.1021/acs.jafc.2c05585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
d-Allulose is an attractive rare sugar that can be used as a low-calorie sweetener with significant health benefits. To meet the increasing market demands, it is necessary to develop an efficient and extensive microbial fermentation platform for the synthesis of d-allulose. Here, we applied a comprehensive systematic engineering strategy in Bacillus subtilis WB600 by introducing d-allulose 3-epimerase (DAEase), combined with the deactivation of fruA, levDEFG, and gmuE, to balance the metabolic network for the efficient production of d-allulose. This resulting strain initially produced 3.24 g/L of d-allulose with a yield of 0.93 g of d-allulose/g d-fructose. We further screened and obtained a suitable dual promoter combination and performed fine-tuning of its spacer region. After 64 h of fed-batch fermentation, the optimized engineered B. subtilis produced d-allulose at titers of 74.2 g/L with a yield of 0.93 g/g and a conversion rate of 27.6%. This d-allulose production strain is a promising platform for the industrial production of rare sugar.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, P. R. China
| | - Meijing Wei
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, P. R. China
| | - Xiaoxuan Sun
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, P. R. China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, P. R. China
| | - Lijun Guan
- Institute of Food Processing, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, P. R. China
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, P. R. China
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Song Y, He S, Jopkiewicz A, Setroikromo R, van Merkerk R, Quax WJ. Development and application of CRISPR-based genetic tools in Bacillus species and Bacillus phages. J Appl Microbiol 2022; 133:2280-2298. [PMID: 35797344 PMCID: PMC9796756 DOI: 10.1111/jam.15704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/02/2022] [Accepted: 07/06/2022] [Indexed: 01/07/2023]
Abstract
Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) system has been developed into a precise and efficient genome editing tool. Since its discovery as an adaptive immune system in prokaryotes, it has been applied in many different research fields including biotechnology and medical sciences. The high demand for rapid, highly efficient and versatile genetic tools to thrive in bacteria-based cell factories accelerates this process. This review mainly focuses on significant advancements of the CRISPR system in Bacillus subtilis, including the achievements in gene editing, and on problems still remaining. Next, we comprehensively summarize this genetic tool's up-to-date development and utilization in other Bacillus species, including B. licheniformis, B. methanolicus, B. anthracis, B. cereus, B. smithii and B. thuringiensis. Furthermore, we describe the current application of CRISPR tools in phages to increase Bacillus hosts' resistance to virulent phages and phage genetic modification. Finally, we suggest potential strategies to further improve this advanced technique and provide insights into future directions of CRISPR technologies for rendering Bacillus species cell factories more effective and more powerful.
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Affiliation(s)
- Yafeng Song
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern ChinaInstitute of Microbiology, Guangdong Acadamy of SciencesGuangzhouChina
| | - Siqi He
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Anita Jopkiewicz
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Wim J. Quax
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
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Optimization of Signal Peptide via Site-Directed Mutagenesis for Enhanced Secretion of Heterologous Proteins in Lactococcus lactis. Int J Mol Sci 2022; 23:ijms231710044. [PMID: 36077441 PMCID: PMC9456127 DOI: 10.3390/ijms231710044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022] Open
Abstract
Secretion efficiency of heterologous proteins in the Generally Regarded As Safe (GRAS) Lactococcus lactis is often reported to be insufficiently low due to limitations such as poor targeting and translocation by the signal peptide or degradation by the host proteases. In this study, the secretion efficiency in the host was enhanced through the utilization of a heterologous signal peptide (SP) SPK1 of Pediococcus pentosaceus. The SPK1 was subjected to site-directed mutations targeting its tripartite N-, H-, and C-domains, and the effect on secretion efficiency as compared to the wild-type SPK1 and native lactococcal USP45 was determined on a reporter nuclease (NUC) of Staphylococcus aureus. A Fluorescence Resonance Energy Transfer (FRET) analysis indicated that four out of eight SPK1 variants successfully enhanced the secretion of NUC, with the best mutant, SPKM19, showing elevated secretion efficiency up to 88% (or by 1.4-fold) and an improved secretion activity yield of 0.292 ± 0.122 U/mL (or by 1.7-fold) compared to the wild-type SPK1. Modifications of the SPK1 at the cleavage site C-domain region had successfully augmented the secretion efficiency. Meanwhile, mutations in the H-domain region had resulted in a detrimental effect on the NUC secretion. The development of heterologous SPs with better efficacy than the USP45 has been demonstrated in this study for enhanced secretion of heterologous production and mucosal delivery applications in the lactococcal host.
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26
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Le NTP, Phan TTP, Phan HTT, Truong TTT, Schumann W, Nguyen HD. Influence of N-terminal His-tags on the production of recombinant proteins in the cytoplasm of Bacillus subtilis. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2022; 35:e00754. [PMID: 35911505 PMCID: PMC9326129 DOI: 10.1016/j.btre.2022.e00754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/28/2022] [Accepted: 07/14/2022] [Indexed: 05/26/2023]
Abstract
The influence of fusion tags to produce recombinant proteins in the cytoplasm of Bacillus subtilis is not well-studied as in E. coli. This study aimed to investigate the influence of His-tags with different codons on the protein production levels of the high expression gene (gfp+) and low expression gene (egfp) in the cytoplasm of B. subtilis cells. We used three different N-terminal His-tags, M-6xHis, MRGS-8xHis and MEA-8xHis, to investigate their effects on the production levels of GFP variants under the control of the Pgrac212 in B. subtilis. The fusions of His-tags with GFP+ caused a reduction compared to the construct without His-tag. When three His-tags fused with egfp, the EGFP production levels were significantly increased up to 3.5-, 12-, and 15-fold. This study suggested that His-tag at the N-terminus could enhance the protein production for the low expression gene and reduce that of the high expression gene in B. subtilis.
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Affiliation(s)
- Ngan Thi Phuong Le
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Trang Thi Phuong Phan
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh City, Vietnam
| | - Hanh Thi Thu Phan
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Tuom Thi Tinh Truong
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Cancer research laboratory, University of Science, Ho Chi Minh City, Vietnam
| | - Wolfgang Schumann
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Hoang Duc Nguyen
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
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27
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Jiang C, Ye C, Liu Y, Huang K, Jiang X, Zou D, Li L, Han W, Wei X. Genetic engineering for enhanced production of a novel alkaline protease BSP-1 in Bacillus amyloliquefaciens. Front Bioeng Biotechnol 2022; 10:977215. [PMID: 36110310 PMCID: PMC9468883 DOI: 10.3389/fbioe.2022.977215] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Alkaline protease has been widely applied in food, medicine, environmental protection and other industrial fields. However, the current activity and yield of alkaline protease cannot meet the demand. Therefore, it is important to identify new alkaline proteases with high activity. In this study, we cloned a potential alkaline protease gene bsp-1 from a Bacillus subtilis strain isolated in our laboratory. BSP-1 shows the highest sequence similarity to subtilisin NAT (S51909) from B. subtilis natto. Then, we expressed BSP-1 in Bacillus amyloliquefaciens BAX-9 and analyzed the protein expression level under a collection of promoters. The results show that the P43 promoter resulted in the highest transcription level, protein level and enzyme activity. Finally, we obtained a maximum activity of 524.12 U/mL using the P43 promoter after fermentation medium optimization. In conclusion, this study identified an alkaline protease gene bsp-1 from B. subtilis and provided a new method for high-efficiency alkaline protease expression in B. amyloliquefaciens.
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Affiliation(s)
- Cong Jiang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Changwen Ye
- Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou, China
| | - Yongfeng Liu
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Kuo Huang
- Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou, China
| | - Xuedeng Jiang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Dian Zou
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Lu Li
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuetuan Wei
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Xuetuan Wei,
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Aliivibrio fischeri L-Asparaginase production by engineered Bacillus subtilis: a potential new biopharmaceutical. Bioprocess Biosyst Eng 2022; 45:1635-1644. [PMID: 35974197 DOI: 10.1007/s00449-022-02769-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/04/2022] [Indexed: 11/02/2022]
Abstract
L-Asparaginase (L-ASNase) is an enzyme applied in the treatment of lymphoid malignancies. However, an innovative L-ASNase with high yield and lower side effects than the commercially available preparations are still a market requirement. Here, a new-engineered Bacillus subtilis strain was evaluated for Aliivibrio fischeri L-ASNase II production, being the bioprocess development and the enzyme characterization studied. The pBS0E plasmid replicative in Bacillus sp and containing PxylA promoter inducible by xylose and its repressive molecule sequence (XylR) was used for the genetic modification. Initially, cultivations were carried out in orbital shaker, and then the process was scaled up to stirred tank bioreactor (STB). After the bioprocess, the cells were recovered and submitted to ultrasound sonication for cells disruption and intracellular enzyme recovery. The enzymatic extract was characterized to assess its biochemical, kinetic and thermal properties using L-Asparagine and L-Glutamine as substrates. The results indicated the potential enzyme production in STB achieving L-ASNase activity up to 1.539 U mL-1. The enzymatic extract showed an optimum pH of 7.5, high L-Asparagine affinity (Km = 1.2275 mmol L-1) and low L-Glutaminase activity (0.568-0.738 U mL-1). In addition, thermal inactivation was analyzed by two different Kinect models to elucidate inactivation mechanisms, low kinetic thermal inactivation constants for 25 ºC and 37 ºC (0.128 and 0.148 h-1, respectively) indicate an elevated stability. The findings herein show that the produced recombinant L-ASNase has potential to be applied for pharmaceutical purposes.
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29
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Chen Y, Zhang R, Zhang W, Xu Y. Alanine aminopeptidase from Bacillus licheniformis E7 expressed in Bacillus subtilis efficiently hydrolyzes soy protein to small peptides and free amino acids. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Wang G, Guo Z, Zhang X, Wu H, Bai X, Zhang H, Hu R, Han S, Pang Y, Gao Z, Yan L, Huang C, Zhang L, Pan C, Liu X. Heterologous expression of pediocin/papA in Bacillus subtilis. Microb Cell Fact 2022; 21:104. [PMID: 35643507 PMCID: PMC9148482 DOI: 10.1186/s12934-022-01829-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/16/2022] [Indexed: 11/16/2022] Open
Abstract
Listeria monocytogenes is a food-borne pathogen. Pediocin is a group IIα bacteriocin with anti-listeria activity that is naturally produced by Pediococcus acidilactic and Lactobacillus plantarum. The pedA/papA gene encodes pediocin/plantaricin. In native hosts, the expression and secretion of active PedA/PapA protein rely on the accessory protein PedC/PapC and ABC transporter PedD/PapD on the same operon. The excretion machines were also necessary for pediocin protein expression in heterologous hosts of E. coli, Lactobacillus lactis, and Corynebacterium glutamicum. In this study, two vectors carrying the codon sequence of the mature PapA peptide were constructed, one with and one without a His tag. Both fragments were inserted into the plasmid pHT43 and transformed into Bacillus subtilis WB800N. The strains were induced with IPTG to secrete the fused proteins PA1 and PA2. Supernatants from both recombinant strains can inhibit Listeria monocytogenes ATCC54003 directly. The fused protein possesses inhibition activity as a whole dispense with removal of the leading peptide. This is the first report of active pediocin/PapA expression without the assistance of PedCD/PapCD in heterogeneous hosts. In addition, the PA1 protein can be purified by nickel-nitrilotriacetic acid (Ni-NTA) metal affinity chromatography.
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Shafaati M, Ghorbani M, Mahmoodi M, Ebadi M, Jalalirad R. Expression and characterization of hemagglutinin-neuraminidase protein from Newcastle disease virus in Bacillus subtilis WB800. J Genet Eng Biotechnol 2022; 20:77. [PMID: 35608724 PMCID: PMC9130408 DOI: 10.1186/s43141-022-00357-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/02/2022] [Indexed: 11/13/2022]
Abstract
Background Newcastle disease virus (NDV) belongs to the genus Avaluvirus and Paramyxoviridae family, and it can cause acute, highly contagious Newcastle disease in poultry. The two proteins, haemagglutinin neuraminidase (HN) and Fusion (F), are the main virulence factor of the virus and play an essential role in immunogenicity against the virus. In most paramyxoviruses, the F protein requires HN protein to fuse the membrane, and HN proteins substantially enhance the viruses’ fusion activity. Results The present study describes the successful cloning and expression of HN protein from NDV in Bacillus subtilis WB800 using the modified shuttle vector pHT43. HN coding sequence was cloned into the pGet II vector. It was then subcloned into the PHT43 shuttle vector and transferred to Escherichia coli for replication. The recombinant plasmid was extracted from E. coli and used to transform B. subtilis by electroporation. After induction of recombinant B. subtilis by IPTG, total cell protein and the protein secreted into the media were analysed through a time course using SDS-PAGE. The expressed HN protein was purified using cation exchange chromatography followed by metal affinity chromatography, using the 6× His epitope introduced at the carboxyl terminus of the recombinant protein. The accuracy of the PHT43-HN construct was confirmed by sequencing and enzymatic digestion. SDS-PAGE results showed that the recombinant HN protein was successfully expressed and secreted into the medium. Moreover, the purified HN protein showed neuraminidase activity with characteristics similar to the indigenous HN NDV protein. B. subtilis is a free endotoxin host that could be a favourite prokaryotic platform for producing the recombinant HN protein. Conclusion The establishment of this expression and purification system has allowed us to explore further the biochemical characteristics of HN protein and obtain material that could be suitable for a new production of NDV candidate vaccine with high immunogenicity.
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Affiliation(s)
- Mohammadreza Shafaati
- Department of Cellular & Molecular Biology, Faculty of Basic Sciences, Hamedan Branch, Islamic Azad University, Hamedan, Iran
| | - Masoud Ghorbani
- Pasteur Institute of Iran, Production and Research Complex, Department of Research and Development, Kilometre 25 Karaj-Tehran Highway, Karaj, Alborz, 31599, Iran.
| | - Minoo Mahmoodi
- Department of Cellular & Molecular Biology, Faculty of Basic Sciences, Hamedan Branch, Islamic Azad University, Hamedan, Iran
| | - Mostafa Ebadi
- Department of Biology, Faculty of Sciences, Damaghan Branch, Islamic Azad University, Damghan, Semnan, Iran
| | - Reza Jalalirad
- Pasteur Institute of Iran, Production and Research Complex, Department of Research and Development, Kilometre 25 Karaj-Tehran Highway, Karaj, Alborz, 31599, Iran
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Rajabi M, Nourisanami F, Ghadikolaei KK, Changizian M, Noghabi KA, Zahiri HS. Metagenomic psychrohalophilic xylanase from camel rumen investigated for bioethanol production from wheat bran using Bacillus subtilis AP. Sci Rep 2022; 12:8152. [PMID: 35581279 PMCID: PMC9114127 DOI: 10.1038/s41598-022-11412-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 04/25/2022] [Indexed: 11/09/2022] Open
Abstract
Bioethanol produced from lignocellulosic biomass is regarded as a clean and sustainable energy source. The recalcitrant structure of lignocellulose is a major drawback to affordable bioethanol production from plant biomass. In this study, a novel endo-1,4-xylanase, named Xyn-2, from the camel rumen metagenome, was characterized and evaluated for hydrolysis of agricultural wastes. The enzyme was identified as a psychrohalophilic xylanase with maximum activity at 20 °C, keeping 58% of the activity at 0 °C, and exhibiting twice as much activity in 0.5–4 M NaCl concentrations. Xyn-2 was able to hydrolyze wheat bran (100%), sunflower-seed shell (70%), wheat straw (56%), rice straw (56%), and rice bran (41%), in the relative order of efficiency. Besides, the ethanologenic B. subtilis AP was evaluated without and with Xyn-2 for bioethanol production from wheat bran. The strain was able to produce 5.5 g/L ethanol with a yield of 22.6% in consolidated bioprocessing (CBP). The contribution of Xyn-2 to ethanol production of B. subtilis AP was studied in an SSF system (simultaneous saccharification and fermentation) giving rise to a significant increase in ethanol production (p ≤ 0.001) to a final concentration of 7.3 g/L with a yield of 26.8%. The results revealed that the camel rumen metagenome might be an invaluable source of novel xylanolytic enzymes with potential application in lignocellulosic biomass valorization. At the same time, the results suggest that B. subtilis with a diverse carbon-source preference and sophisticated systems for production and secretion of enzymes might be a promising candidate for strain development for bioethanol production from plant biomass. It might be assumed that the fortification of B. subtilis enzymatic arsenal with select xylanolytic enzymes from camel rumen metagenome may have a great impact on bioethanol production.
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Affiliation(s)
- Marzieh Rajabi
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Farahdokht Nourisanami
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Kamran Khalili Ghadikolaei
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Mohammad Changizian
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Kambiz Akbari Noghabi
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Hossein Shahbani Zahiri
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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Jeong DE, Kim MS, Kim HR, Choi SK. Cell Factory Engineering of Undomesticated Bacillus Strains Using a Modified Integrative and Conjugative Element for Efficient Plasmid Delivery. Front Microbiol 2022; 13:802040. [PMID: 35558120 PMCID: PMC9086855 DOI: 10.3389/fmicb.2022.802040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/14/2022] [Indexed: 11/29/2022] Open
Abstract
A large number of Bacillus strains have been isolated from various environments and many of them have great potential as cell factories. However, they have been rarely developed as cell factories due to their poor transformation efficiency. In this study, we developed a highly efficient plasmid delivery system for undomesticated Bacillus strains using a modified integrative and conjugative element (MICE), which was designed to be activated by an inducer, prevent self-transfer, and deliver desired plasmids to the recipient cells. The MICE system was demonstrated to successfully introduce a gfp-containing plasmid into all 41 undomesticated Bacillus subtilis strains tested and eight other Bacillus species. The MICE was used to deliver a cytosine base editor (CBE)-based multiplex genome-editing tool for the cell factory engineering of the Bacillus species. The introduced CBE enabled one-step inactivation of the major extracellular protease genes of the tested strains. The engineered strains were used as hosts for heterologous expression of nattokinase, which resulted in various enzyme expression levels. The results suggested that the MICE and CBE systems can be powerful tools for genetic engineering of undomesticated Bacillus strains, and greatly contribute to the expansion of the Bacillus cell factory.
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Affiliation(s)
- Da-Eun Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Man Su Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, South Korea
| | - Ha-Rim Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Soo-Keun Choi
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, South Korea
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Singh N, Singh V, Singh MP. Microbial degradation of lignocellulosic biomass for bioenergy production: A metagenomic-based approach. BIOCATAL BIOTRANSFOR 2022. [DOI: 10.1080/10242422.2022.2056451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nidhi Singh
- Centre of Bioinformatics, University of Allahabad, Allahabad, India
- School of Biochemical Engineering, IIT (BHU), Varanasi, India
| | - Veer Singh
- Centre of Biotechnology, University of Allahabad, Allahabad, India
| | - Mohan P. Singh
- Centre of Biotechnology, University of Allahabad, Allahabad, India
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Production of Vitamin K by Wild-Type and Engineered Microorganisms. Microorganisms 2022; 10:microorganisms10030554. [PMID: 35336129 PMCID: PMC8954062 DOI: 10.3390/microorganisms10030554] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
Vitamin K is a fat-soluble vitamin that mainly exists as phylloquinone or menaquinone in nature. Vitamin K plays an important role in blood clotting and bone health in humans. For use as a nutraceutical, vitamin K is produced by natural extraction, chemical synthesis, and microbial fermentation. Natural extraction and chemical synthesis methods for vitamin K production have limitations, such as low yield of products and environmental concerns. Microbial fermentation is a more sustainable process for industrial production of natural vitamin K than two other methods. Recent advanced genetic technology facilitates industrial production of vitamin K by increasing the yield and productivity of microbial host strains. This review covers (i) general information about vitamin K and microbial host, (ii) current titers of vitamin K produced by wild-type microorganisms, and (iii) vitamin K production by engineered microorganisms, including the details of strain engineering strategies. Finally, current limitations and future directions for microbial production of vitamin K are also discussed.
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To HTA, Chhetri V, Settachaimongkon S, Prakitchaiwattana C. Stress tolerance-Bacillus with a wide spectrum bacteriocin as an alternative approach for food bio-protective culture production. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108598] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Zhang K, Su L, Wu J. Enhancing Extracellular Pullulanase Production in Bacillus subtilis Through dltB Disruption and Signal Peptide Optimization. Appl Biochem Biotechnol 2022; 194:1206-1220. [PMID: 34652585 DOI: 10.1007/s12010-021-03617-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
Bacillus subtilis has many attributes that make it a popular host for recombinant protein production. Although its protein production ability has been enhanced through protease gene disruption, residual proteases like quality control HtrA and HtrB can limit protein yield by degrading inadequately folded proteins present during overexpression. In this study, two strategies were employed to increase production of industrial enzyme pullulanase: enhancing extracellular pullulanase folding and optimizing its signal peptide. The hypothesis was that disruption of dltB gene of expression host B. subtilis WS9 would enhance recombinant extracellular folding by increasing cation binding to the cell's outer envelope. Consistent with this hypothesis, disrupting dltB enhanced pullulanase production by 49% in shake-flask cultures. The disruption also enhanced extracellular α-CGTase and β-CGTase production by 25% and 35%, respectively. Then, more effective signal peptide for pullulanase production was identified through high-throughput screening of 173 unique B. subtilis signal peptides. Replacing the native signal peptide of pullulanase with that encoded by ywtF increased extracellular pullulanase activity by an additional 12%. Three-liter fermenter scale-up production yielded the highest extracellular pullulanase activity reported to date: 8037.91 U·mL-1. This study highlights the usefulness of dltB deletion and signal peptide optimization in enhancing extracellular protein production.
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Affiliation(s)
- Kang Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
- International Joint Laboratory On Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
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Cho HY, Nam MS, Hong HJ, Song WS, Yoon SI. Structural and Biochemical Analysis of the Furan Aldehyde Reductase YugJ from Bacillus subtilis. Int J Mol Sci 2022; 23:ijms23031882. [PMID: 35163804 PMCID: PMC8836905 DOI: 10.3390/ijms23031882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/29/2022] [Accepted: 02/04/2022] [Indexed: 02/05/2023] Open
Abstract
NAD(H)/NADP(H)-dependent aldehyde/alcohol oxidoreductase (AAOR) participates in a wide range of physiologically important cellular processes by reducing aldehydes or oxidizing alcohols. Among AAOR substrates, furan aldehyde is highly toxic to microorganisms. To counteract the toxic effect of furan aldehyde, some bacteria have evolved AAOR that converts furan aldehyde into a less toxic alcohol. Based on biochemical and structural analyses, we identified Bacillus subtilis YugJ as an atypical AAOR that reduces furan aldehyde. YugJ displayed high substrate specificity toward 5-hydroxymethylfurfural (HMF), a furan aldehyde, in an NADPH- and Ni2+-dependent manner. YugJ folds into a two-domain structure consisting of a Rossmann-like domain and an α-helical domain. YugJ interacts with NADP and Ni2+ using the interdomain cleft of YugJ. A comparative analysis of three YugJ structures indicated that NADP(H) binding plays a key role in modulating the interdomain dynamics of YugJ. Noticeably, a nitrate ion was found in proximity to the nicotinamide ring of NADP in the YugJ structure, and the HMF-reducing activity of YugJ was inhibited by nitrate, providing insights into the substrate-binding mode of YugJ. These findings contribute to the characterization of the YugJ-mediated furan aldehyde reduction mechanism and to the rational design of improved furan aldehyde reductases for the biofuel industry.
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Affiliation(s)
- Hye Yeon Cho
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (H.Y.C.); (M.S.N.); (H.J.H.)
| | - Mi Sun Nam
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (H.Y.C.); (M.S.N.); (H.J.H.)
| | - Ho Jeong Hong
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (H.Y.C.); (M.S.N.); (H.J.H.)
| | - Wan Seok Song
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Korea
- Correspondence: (W.S.S.); (S.-i.Y.)
| | - Sung-il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (H.Y.C.); (M.S.N.); (H.J.H.)
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Korea
- Correspondence: (W.S.S.); (S.-i.Y.)
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Improving the Biocontrol Potential of Endophytic Bacteria Bacillus subtilis with Salicylic Acid against Phytophthora infestans-Caused Postharvest Potato Tuber Late Blight and Impact on Stored Tubers Quality. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Potato (Solanum tuberosum L.) tubers are a highly important food crop in many countries due to their nutritional value and health-promoting properties. Postharvest disease caused by Phytophthora infestans leads to the significant decay of stored potatoes. The main objective of this study was to evaluate the effects of the endophytic bacteria, Bacillus subtilis (strain 10–4), or its combination with salicylic acid (SA), on some resistance and quality traits of stored Ph. infestans-infected potato tubers. The experiments were conducted using hydroponically grown potato mini-tubers, infected prior to storage with Ph. infestans, and then coated with B. subtilis, alone and in combination with SA, which were then stored for six months. The results revealed that infection with Ph. infestans significantly increased tuber late blight incidence (up to 90–100%) and oxidative and osmotic damage (i.e., malondialdehyde and proline) in tubers. These phenomena were accompanied by a decrease in starch, reducing sugars (RS), and total dry matter (TDM) contents and an increase in amylase (AMY) activity. Moreover, total glycoalkaloids (GA) (α-solanine, α-chaconine) notably increased in infected tubers, exceeding (by 1.6 times) permissible safe levels (200 mg/kg FW). Treatments with B. subtilis or its combination with SA decreased Ph. infestans-activated tuber late blight incidence (by 30–40%) and reduced oxidative and osmotic damages (i.e., malondialdehyde and proline) and AMY activity in stored, infected tubers. Additionally, these treatments decreased pathogen-activated GA accumulation and increased ascorbic acid in stored tubers. Thus, the results indicated that endophytic bacteria B. subtilis, individually, and especially in combination with SA, have the potential to increase potato postharvest resistance to late blight and improve tuber quality in long-term storage.
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Hioki T, Yamashita D, Tohata M, Endo K, Kawahara A, Okuda M. Heterologous production of active form of beta-lytic protease by Bacillus subtilis and improvement of staphylolytic activity by protein engineering. Microb Cell Fact 2021; 20:231. [PMID: 34963446 PMCID: PMC8715609 DOI: 10.1186/s12934-021-01724-x] [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: 09/29/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
Background Most of the proteases classified into the M23 family in the MEROPS database exhibit staphylolytic activity and have potential as antibacterial agents. The M23 family is further classified into two subfamilies, M23A and M23B. Proteases of the M23A subfamily are thought to lack the capacity for self-maturation by auto-processing of a propeptide, which has been a challenge in heterologous production and application research. In this study, we investigated the heterologous expression, in Bacillus subtilis, of the Lysobacter enzymogenes beta-lytic protease (BLP), a member of the M23A subfamily. Results We found that B. subtilis can produce BLP in its active form. Two points were shown to be important for the production of BLP in B. subtilis. The first was that the extracellular proteases produced by the B. subtilis host are essential for BLP maturation. When the host strain was deficient in nine extracellular proteases, pro-BLP accumulated in the supernatant. This observation suggested that BLP lacks the capacity for self-maturation and that some protease from B. subtilis contributes to the cleavage of the propeptide of BLP. The second point was that the thiol-disulfide oxidoreductases BdbDC of the B. subtilis host are required for efficient secretory production of BLP. We infer that intramolecular disulfide bonds play an important role in the formation of the correct BLP conformation during secretion. We also achieved efficient protein engineering of BLP by utilizing the secretory expression system in B. subtilis. Saturation mutagenesis of Gln116 resulted in a Q116H mutant with enhanced staphylolytic activity. The minimum bactericidal concentration (MBC) of the wild-type BLP and the Q116H mutant against Staphylococcus aureus NCTC8325 was 0.75 μg/mL and 0.375 μg/mL, respectively, and the MBC against Staphylococcus aureus ATCC43300 was 6 μg/mL and 3 μg/mL, respectively. Conclusions In this study, we succeeded in the secretory production of BLP in B. subtilis. To our knowledge, this work is the first report of the successful heterologous production of BLP in its active form, which opens up the possibility of industrial use of BLP. In addition, this study proposes a new strategy of using the extracellular proteases of B. subtilis for the maturation of heterologous proteins. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01724-x.
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Affiliation(s)
- Takahiro Hioki
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640-8580, Japan.
| | - Daichi Yamashita
- Biological Science Research, Kao Corporation, Haga , Tochigi, 2606 Akabane, Ichikai321-3497, Japan
| | - Masatoshi Tohata
- Safety Science Research, Kao Corporation, 2606 Akabane, Ichikai, Haga, Tochigi, 321-3497, Japan
| | - Keiji Endo
- Biological Science Research, Kao Corporation, Haga , Tochigi, 2606 Akabane, Ichikai321-3497, Japan
| | - Akihito Kawahara
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640-8580, Japan
| | - Mitsuyoshi Okuda
- Biological Science Research, Kao Corporation, Haga , Tochigi, 2606 Akabane, Ichikai321-3497, Japan
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Khosravi F, Khaleghi M, Naghavi H. Screening and identification of cellulose-degrading bacteria from soil and leaves at Kerman province, Iran. Arch Microbiol 2021; 204:88. [PMID: 34961888 DOI: 10.1007/s00203-021-02713-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022]
Abstract
Cellulosic biomass is considered one of the most promising sources for the production of alternative renewable bioenergy and other valuable products. Identification and optimization of strains with high enzymatic activity that can overcome constraints imposed by the cellulosic structure is an essential step in the development of new biotechnologies. The aim of this study was to isolate and identify thermophilic (50 °C) and mesophilic (37 °C) cellulolytic bacteria from soil and leaves samples at Kerman, Iran. Degrader bacteria were isolated using serial dilution and pour plate method. Media contained carboxymethylcellulose (CMC), and filter paper was used as sources of carbon. Totally 22 mesophilic and 17 thermophilic bacterial strains which produced clear zones were further identified by morphological and biochemical tests. Screening of purified bacteria was performed to identify cellulase-producing bacteria by Congo red test. These bacteria were compared to each other based on cellulase activity, the percentage of growth, and extracellular protein amounts. The strains with the highest enzymatic activity were determined by the DNS method. The isolated US5 and US7 grew rapidly, and produced cellulase. The US5 created the largest clear zones (7 mm). Besides, these strains were selected for analysis of 16S rRNA sequence. The results showed that selected bacteria strains belong to Brevibacillus borstelensis. The B. borstelensis strains isolated in this study showed a suitable cellulase enzyme activity.
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Affiliation(s)
- Farshid Khosravi
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Mouj Khaleghi
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hormazd Naghavi
- Soil and Water Research, Kerman Agricultural and Natural Resources Research and Education Center, AREEO, Kerman, Iran
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Qi X, Yan W, Cao Z, Ding M, Yuan Y. Current Advances in the Biodegradation and Bioconversion of Polyethylene Terephthalate. Microorganisms 2021; 10:39. [PMID: 35056486 PMCID: PMC8779501 DOI: 10.3390/microorganisms10010039] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 01/04/2023] Open
Abstract
Polyethylene terephthalate (PET) is a widely used plastic that is polymerized by terephthalic acid (TPA) and ethylene glycol (EG). In recent years, PET biodegradation and bioconversion have become important in solving environmental plastic pollution. More and more PET hydrolases have been discovered and modified, which mainly act on and degrade the ester bond of PET. The monomers, TPA and EG, can be further utilized by microorganisms, entering the tricarboxylic acid cycle (TCA cycle) or being converted into high value chemicals, and finally realizing the biodegradation and bioconversion of PET. Based on synthetic biology and metabolic engineering strategies, this review summarizes the current advances in the modified PET hydrolases, engineered microbial chassis in degrading PET, bioconversion pathways of PET monomers, and artificial microbial consortia in PET biodegradation and bioconversion. Artificial microbial consortium provides novel ideas for the biodegradation and bioconversion of PET or other complex polymers. It is helpful to realize the one-step bioconversion of PET into high value chemicals.
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Affiliation(s)
- Xinhua Qi
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (X.Q.); (W.Y.); (Z.C.); (Y.Y.)
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Wenlong Yan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (X.Q.); (W.Y.); (Z.C.); (Y.Y.)
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Zhibei Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (X.Q.); (W.Y.); (Z.C.); (Y.Y.)
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Mingzhu Ding
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (X.Q.); (W.Y.); (Z.C.); (Y.Y.)
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (X.Q.); (W.Y.); (Z.C.); (Y.Y.)
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
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Qi X, Ma Y, Chang H, Li B, Ding M, Yuan Y. Evaluation of PET Degradation Using Artificial Microbial Consortia. Front Microbiol 2021; 12:778828. [PMID: 35003008 PMCID: PMC8733400 DOI: 10.3389/fmicb.2021.778828] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/06/2021] [Indexed: 01/30/2023] Open
Abstract
Polyethylene terephthalate (PET) biodegradation is regarded as an environmentally friendly degradation method. In this study, an artificial microbial consortium composed of Rhodococcus jostii, Pseudomonas putida and two metabolically engineered Bacillus subtilis was constructed to degrade PET. First, a two-species microbial consortium was constructed with two engineered B. subtilis that could secrete PET hydrolase (PETase) and monohydroxyethyl terephthalate hydrolase (MHETase), respectively; it could degrade 13.6% (weight loss) of the PET film within 7 days. A three-species microbial consortium was further obtained by adding R. jostii to reduce the inhibition caused by terephthalic acid (TPA), a breakdown product of PET. The weight of PET film was reduced by 31.2% within 3 days, achieving about 17.6% improvement compared with the two-species microbial consortium. Finally, P. putida was introduced to reduce the inhibition caused by ethylene glycol (EG), another breakdown product of PET, obtaining a four-species microbial consortium. With the four-species consortium, the weight loss of PET film reached 23.2% under ambient temperature. This study constructed and evaluated the artificial microbial consortia in PET degradation, which demonstrated the great potential of artificial microbial consortia in the utilization of complex substrates, providing new insights for biodegradation of complex polymers.
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Affiliation(s)
- Xinhua Qi
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Yuan Ma
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Hanchen Chang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Bingzhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Mingzhu Ding
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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44
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Tang K, Beyer HM, Zurbriggen MD, Gärtner W. The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters. Chem Rev 2021; 121:14906-14956. [PMID: 34669383 PMCID: PMC8707292 DOI: 10.1021/acs.chemrev.1c00194] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 12/15/2022]
Abstract
This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.
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Affiliation(s)
- Kun Tang
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Hannes M. Beyer
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute
of Synthetic Biology and CEPLAS, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
| | - Wolfgang Gärtner
- Retired: Max Planck Institute
for Chemical Energy Conversion. At present: Institute for Analytical Chemistry, University
Leipzig, Linnéstrasse
3, 04103 Leipzig, Germany
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Pramod S, Thommana RT, Kulanthaivelu Kanagam H, Suresh Kumar A, S SK, Elangovan E, Perumal K. Data on the genome of Bacillus subtilis A1- Midalam from beach soil. Data Brief 2021; 39:107552. [PMID: 34820494 PMCID: PMC8601982 DOI: 10.1016/j.dib.2021.107552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 11/05/2022] Open
Abstract
The draft genome sequence of Bacillus subtilis A1, isolated from beach soil, has been shown to produce biofilm. The genome size is 4,215,114 bp with an average G+C content of 43.5%. The genome of Bacillus subtilis A1 has 4413 total genes which include 4166 protein-coding sequences, 126 pseudo genes, 10 rRNA genes with 3 operons (5S, 16S and 23S), 86 tRNA genes and 5 noncoding RNA (ncRNA) genes. The genome contains genes coding for surfactin, fengycin, bacillaene, sublancin 168, bacillibactin, subtilosin A, bacilysin. The whole genome project has been deposited in GenBank under the accession number CP075344.1. The raw data is available at https://www.ncbi.nlm.nih.gov/nuccore/CP075344.1.
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Affiliation(s)
- Sneha Pramod
- Biochemistry and Molecular Biology Department, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, USA
| | - Rhea Thomas Thommana
- Department of Food and Bioproduct Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Canada
| | | | - Ashmita Suresh Kumar
- Department of Cancer Biology, Wake Forest School of Medicine, North Carolina, USA
| | - Santha Kalaikumari S
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Elavarashi Elangovan
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research, Porur, Tamilnadu, India
| | - Kumar Perumal
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research, Porur, Tamilnadu, India
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46
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Far BE, Ragheb M, Rahbar R, Mafakher L, Nojookambari NY, Achinas S, Yazdansetad S. Cloning and expression of Staphylococcus simulans lysostaphin enzyme gene in Bacillus subtilis WB600. AIMS Microbiol 2021; 7:271-283. [PMID: 34708172 PMCID: PMC8500799 DOI: 10.3934/microbiol.2021017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/16/2021] [Indexed: 11/18/2022] Open
Abstract
Lysostaphin is a glycylglycine endopeptidase, secreted by Staphylococcus simulans, capable of specifically hydrolyzing pentaglycine crosslinks present in the peptidoglycan of the Staphylococcus aureus cell wall. In this paper, we describe the cloning and expression of the lysostaphin enzyme gene in Bacillus subtilis WB600 host using pWB980 expression system. Plasmid pACK1 of S. simulans was extracted using the alkaline lysis method. Lysostaphin gene was isolated by PCR and cloned into pTZ57R/T-Vector, then transformed into Escherichia coli DH5α. The amplified gene fragment and uncloned pWB980 vector were digested using PstI and XbaІ enzymes and purified. The restricted gene fragment was ligated into the pWB980 expression vector by the standard protocols, then the recombinant plasmid was transformed into B. subtilis WB600 using electroporation method. The recombinant protein was evaluated by the SDS-PAGE method and confirmed by western immunoblot. Analysis of the target protein showed a band corresponding to 27-kDa r-lysostaphin. Protein content was estimated 91 mg/L by Bradford assay. The recombinant lysostaphin represented 90% of its maximum activity at 40 °C and displayed good thermostability by keeping about 80% of its maximum activity at 45 °C. Heat residual activity assay of recombinant lysostaphin demonstrated that the enzyme stability was up to 40 °C and showed good stability at 40 °C for 16 h incubation.
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Affiliation(s)
- Babak Elyasi Far
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehran Ragheb
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Rahbar
- Student Research Committee, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ladan Mafakher
- Medical Plant Research Center, Ahvaz Jundishapur University of Medical Science, Ahvaz, Iran
| | - Neda Yousefi Nojookambari
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Spyridon Achinas
- Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Sajjad Yazdansetad
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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47
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Treinen C, Magosch O, Hoffmann M, Klausmann P, Würtz B, Pfannstiel J, Morabbi Heravi K, Lilge L, Hausmann R, Henkel M. Modeling the time course of ComX: towards molecular process control for Bacillus wild-type cultivations. AMB Express 2021; 11:144. [PMID: 34714452 PMCID: PMC8556439 DOI: 10.1186/s13568-021-01306-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/19/2021] [Indexed: 11/30/2022] Open
Abstract
Wild-type cultivations are of invaluable relevance for industrial biotechnology when it comes to the agricultural or food sector. Here, genetic engineering is hardly applicable due to legal barriers and consumer’s demand for GMO-free products. An important pillar for wild-type cultivations displays the genus Bacillus. One of the challenges for Bacillus cultivations is the global ComX-dependent quorum sensing system. Here, molecular process control can serve as a tool to optimize the production process without genetic engineering. To realize this approach, quantitative knowledge of the mechanism is essential, which, however, is often available only to a limited extent. The presented work provides a case study based on the production of cyclic lipopeptide surfactin, whose expression is in dependence of ComX, using natural producer B. subtilis DSM 10 T. First, a surfactin reference process with 40 g/L of glucose was performed as batch fermentation in a pilot scale bioreactor system to gain novel insights into kinetic behavior of ComX in relation to surfactin production. Interestingly, the specific surfactin productivity did not increase linearly with ComX activity. The data were then used to derive a mathematic model for the time course of ComX in dependence of existing biomass, biomass growth as well as a putative ComX-specific protease. The newly adapted model was validated and transferred to other batch fermentations, employing 20 and 60 g/L glucose. The applied approach can serve as a model system for molecular process control strategies, which can thus be extended to other quorum sensing dependent wild-type cultivations.
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48
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Vikromvarasiri N, Shirai T, Kondo A. Metabolic engineering design to enhance (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis based on flux balance analysis. Microb Cell Fact 2021; 20:196. [PMID: 34627250 PMCID: PMC8502337 DOI: 10.1186/s12934-021-01688-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 09/24/2021] [Indexed: 01/18/2023] Open
Abstract
Background Glycerol is a desirable alternative substrate for 2,3-butanediol (2,3-BD) production for sustainable development in biotechnological industries and non-food competitive feedstock. B. subtilis, a “generally recognized as safe” organism that is highly tolerant to fermentation products, is an ideal platform microorganism to engineer the pathways for the production of valuable bio-based chemicals, but it has never been engineered to improve 2,3-BD production from glycerol. In this study, we aimed to enhance 2,3-BD production from glycerol in B. subtilis through in silico analysis. Genome-scale metabolic model (GSM) simulations was used to design and develop the metabolic pathways of B. subtilis. Flux balance analysis (FBA) simulation was used to evaluate the effects of step-by-step gene knockouts to improve 2,3-BD production from glycerol in B. subtilis. Results B. subtilis was bioengineered to enhance 2,3-BD production from glycerol using FBA in a published GSM model of B. subtilis, iYO844. Four genes, ackA, pta, lctE, and mmgA, were knocked out step by step, and the effects thereof on 2,3-BD production were evaluated. While knockout of ackA and pta had no effect on 2,3-BD production, lctE knockout led to a substantial increase in 2,3-BD production. Moreover, 2,3-BD production was improved by mmgA knockout, which had never been investigated. In addition, comparisons between in silico simulations and fermentation profiles of all B. subtilis strains are presented in this study. Conclusions The strategy developed in this study, using in silico FBA combined with experimental validation, can be used to optimize metabolic pathways for enhanced 2,3-BD production from glycerol. It is expected to provide a novel platform for the bioengineering of strains to enhance the bioconversion of glycerol into other highly valuable chemical products. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01688-y.
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Affiliation(s)
- Nunthaphan Vikromvarasiri
- RIKEN Center for Sustainable Resource Science, 1‑7‑22 Suehiro‑cho, Tsurumi‑ku, Yokohama, Kanagawa, 230‑0045, Japan.
| | - Tomokazu Shirai
- RIKEN Center for Sustainable Resource Science, 1‑7‑22 Suehiro‑cho, Tsurumi‑ku, Yokohama, Kanagawa, 230‑0045, Japan
| | - Akihiko Kondo
- RIKEN Center for Sustainable Resource Science, 1‑7‑22 Suehiro‑cho, Tsurumi‑ku, Yokohama, Kanagawa, 230‑0045, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
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49
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Stork DA, Squyres GR, Kuru E, Gromek KA, Rittichier J, Jog A, Burton BM, Church GM, Garner EC, Kunjapur AM. Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights. Nat Commun 2021; 12:5429. [PMID: 34521822 PMCID: PMC8440579 DOI: 10.1038/s41467-021-25691-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/18/2021] [Indexed: 02/08/2023] Open
Abstract
Bacillus subtilis is a model gram-positive bacterium, commonly used to explore questions across bacterial cell biology and for industrial uses. To enable greater understanding and control of proteins in B. subtilis, here we report broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons. We use these systems to achieve click-labelling, photo-crosslinking, and translational titration. These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression, validate a predicted protein-protein binding interface, and begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo. We expect that the establishment of this simple and easily accessible chemical biology system in B. subtilis will help uncover an abundance of biological insights and aid genetic code expansion in other organisms.
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Affiliation(s)
- Devon A Stork
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Georgia R Squyres
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Erkin Kuru
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Katarzyna A Gromek
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jonathan Rittichier
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Aditya Jog
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Briana M Burton
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA.
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
| | - Aditya M Kunjapur
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Chemical and Biological Engineering, University of Delaware, Newark, DE, USA.
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50
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Yang H, Qu J, Zou W, Shen W, Chen X. An overview and future prospects of recombinant protein production in Bacillus subtilis. Appl Microbiol Biotechnol 2021; 105:6607-6626. [PMID: 34468804 DOI: 10.1007/s00253-021-11533-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/12/2021] [Accepted: 08/15/2021] [Indexed: 12/27/2022]
Abstract
Bacillus subtilis is a well-characterized Gram-positive bacterium and a valuable host for recombinant protein production because of its efficient secretion ability, high yield, and non-toxicity. Here, we comprehensively review the recent studies on recombinant protein production in B. subtilis to update and supplement other previous reviews. We have focused on several aspects, including optimization of B. subtilis strains, enhancement and regulation of expression, improvement of secretion level, surface display of proteins, and fermentation optimization. Among them, optimization of B. subtilis strains mainly involves undirected chemical/physical mutagenesis and selection and genetic manipulation; enhancement and regulation of expression comprises autonomous plasmid and integrated expression, promoter regulation and engineering, and fine-tuning gene expression based on proteases and molecular chaperones; improvement of secretion level predominantly involves secretion pathway and signal peptide screening and optimization; surface display of proteins includes surface display of proteins on spores or vegetative cells; and fermentation optimization incorporates medium optimization, process condition optimization, and feeding strategy optimization. Furthermore, we propose some novel methods and future challenges for recombinant protein production in B. subtilis.Key points• A comprehensive review on recombinant protein production in Bacillus subtilis.• Novel techniques facilitate recombinant protein expression and secretion.• Surface display of proteins has significant potential for different applications.
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Affiliation(s)
- Haiquan Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Jinfeng Qu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Wei Zou
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, 644000, Sichuan, China
| | - Wei Shen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xianzhong Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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