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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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2
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Öktem A, Pranoto DA, van Dijl JM. Post-translational secretion stress regulation in Bacillus subtilis is controlled by intra- and extracellular proteases. N Biotechnol 2024; 79:71-81. [PMID: 38158017 DOI: 10.1016/j.nbt.2023.12.009] [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: 10/26/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The Gram-positive bacterium Bacillus subtilis is a prolific producer of industrial enzymes that are effectively harvested from the fermentation broth. However, the high capacity of B. subtilis for protein secretion has so far not been exploited to the full due to particular bottlenecks, including product degradation by extracellular proteases and counterproductive secretion stress responses. To unlock the Bacillus secretion pathway for difficult-to-produce proteins, various cellular interventions have been explored, including genome engineering. Our previous research has shown a superior performance of genome-reduced B. subtilis strains in the production of staphylococcal antigens compared to the parental strain 168. This was attributed, at least in part, to redirected secretion stress responses, including the presentation of elevated levels of the quality control proteases HtrA and HtrB that also catalyse protein folding. Here we show that this relates to the elimination of two homologous serine proteases, namely the cytosolic protease AprX and the extracellular protease AprE. This unprecedented posttranslational regulation of secretion stress effectors, like HtrA and HtrB, by the concerted action of cytosolic and extracellular proteases has important implications for the biotechnological application of microbial cell factories. In B. subtilis, this conclusion is underscored by extracellular degradation of the staphylococcal antigen IsaA by both AprX and AprE. Extracellular activity of the cytosolic protease AprX is remarkable since it shows that not only extracellular, but also intracellular proteases impact extracellular product levels. We therefore conclude that intracellular proteases represent new targets for improved recombinant protein production in microbial cell factories like B. subtilis.
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Affiliation(s)
- Ayşegül Öktem
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Dicky A Pranoto
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands.
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3
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Jeyachandran S, Vibhute P, Kumar D, Ragavendran C. Random mutagenesis as a tool for industrial strain improvement for enhanced production of antibiotics: a review. Mol Biol Rep 2023; 51:19. [PMID: 38100064 DOI: 10.1007/s11033-023-08975-4] [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: 09/29/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
Secondary metabolites are produced by microbes in minimal quantities in the natural environment out of necessity. However, in the pharmaceutical industry, their overproduction becomes essential. To achieve higher yields, genetic modifications are employed to create strains that surpass the productivity of the initially isolated strains. While rational screening and genetic engineering have emerged as valuable practices in recent years, the cost-effective technique of mutagenesis and selection, known as "random screening," remains a preferred method for efficient short-term strain development. This review aims to comprehensively explore all aspects of strain improvement, focusing on why random mutagenesis continues to be widely adopted.
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Affiliation(s)
- Sivakamavalli Jeyachandran
- Lab in Biotechnology & Bio-signal Transduction, Department of Orthodontics, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences (SIMATS), Chennai, Tamil Nadu, 600077, India.
| | - Prachi Vibhute
- PG & Research Department of Biotechnology & Microbiology, National College (Autonomous), Tiruchirappalli, Tamil Nadu, 620001, India
| | - Dinesh Kumar
- Applied Phycology and Biotechnology Division, Marine Algal Research Station, CSIR-Central Salt & Marine Chemical Research Institute, Mandapam, Tamil Nadu, 623 519, India
| | - Chinnasamy Ragavendran
- Department of Cariology, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha Dental College and Hospitals, Saveetha University, Chennai, 600 077, India
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4
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Öktem A, Núñez-Nepomuceno D, Ferrero-Bordera B, Walgraeve J, Seefried M, Gesell Salazar M, Steil L, Michalik S, Maaß S, Becher D, Mäder U, Völker U, van Dijl JM. Enhancing bacterial fitness and recombinant enzyme yield by engineering the quality control protease HtrA of Bacillus subtilis. Microbiol Spectr 2023; 11:e0177823. [PMID: 37819116 PMCID: PMC10715036 DOI: 10.1128/spectrum.01778-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/25/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE In the expanding market of recombinant proteins, microbial cell factories such as Bacillus subtilis are key players. Microbial cell factories experience secretion stress during high-level production of secreted proteins, which can negatively impact product yield and cell viability. The CssRS two-component system and CssRS-regulated quality control proteases HtrA and HtrB play critical roles in the secretion stress response. HtrA has a presumptive dual function in protein quality control by exerting both chaperone-like and protease activities. However, its potential role as a chaperone has not been explored in B. subtilis. Here, we describe for the first time the beneficial effects of proteolytically inactive HtrA on α-amylase yields and overall bacterial fitness.
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Affiliation(s)
- Ayşegül Öktem
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - David Núñez-Nepomuceno
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Borja Ferrero-Bordera
- Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | | | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Leif Steil
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Sandra Maaß
- Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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5
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He B, Sachla AJ, Helmann JD. TerC proteins function during protein secretion to metalate exoenzymes. Nat Commun 2023; 14:6186. [PMID: 37794032 PMCID: PMC10550928 DOI: 10.1038/s41467-023-41896-1] [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: 05/08/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023] Open
Abstract
Cytosolic metalloenzymes acquire metals from buffered intracellular pools. How exported metalloenzymes are appropriately metalated is less clear. We provide evidence that TerC family proteins function in metalation of enzymes during export through the general secretion (Sec-dependent) pathway. Bacillus subtilis strains lacking MeeF(YceF) and MeeY(YkoY) have a reduced capacity for protein export and a greatly reduced level of manganese (Mn) in the secreted proteome. MeeF and MeeY copurify with proteins of the general secretory pathway, and in their absence the FtsH membrane protease is essential for viability. MeeF and MeeY are also required for efficient function of the Mn2+-dependent lipoteichoic acid synthase (LtaS), a membrane-localized enzyme with an extracytoplasmic active site. Thus, MeeF and MeeY, representative of the widely conserved TerC family of membrane transporters, function in the co-translocational metalation of Mn2+-dependent membrane and extracellular enzymes.
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Affiliation(s)
- Bixi He
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, NY, 14853-8101, USA
| | - Ankita J Sachla
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, NY, 14853-8101, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, NY, 14853-8101, USA.
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6
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Välimets S, Pedetti P, Virginia LJ, Hoang MN, Sauer M, Peterbauer C. Secretory expression of recombinant small laccase genes in Gram-positive bacteria. Microb Cell Fact 2023; 22:72. [PMID: 37062846 PMCID: PMC10108450 DOI: 10.1186/s12934-023-02075-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/28/2023] [Indexed: 04/18/2023] Open
Abstract
BACKGROUND Laccases are multicopper enzymes that oxidize a wide range of aromatic and non-aromatic compounds in the presence of oxygen. The majority of industrially relevant laccases are derived from fungi and are produced in eukaryotic expression systems such as Pichia pastoris and Saccharomyces cerevisiae. Bacterial laccases for research purposes are mostly produced intracellularly in Escherichia coli, but secretory expression systems are needed for future applications. Bacterial laccases from Streptomyces spp. are of interest for potential industrial applications because of their lignin degrading activities. RESULTS In this study, we expressed small laccases genes from Streptomyces coelicolor, Streptomyces viridosporus and Amycolatopsis 75iv2 with their native signal sequences in Gram-positive Bacillus subtilis and Streptomyces lividans host organisms. The extracellular activities of ScLac, SvLac and AmLac expressed in S. lividans reached 1950 ± 99 U/l, 812 ± 57 U/l and 12 ± 1 U/l in the presence of copper supplementation. The secretion of the small laccases was irrespective of the copper supplementation; however, activities upon reconstitution with copper after expression were significantly lower, indicating the importance of copper during laccase production. The production of small laccases in B. subtilis resulted in extracellular activity that was significantly lower than in S. lividans. Unexpectedly, AmLac and ScLac were secreted without their native signal sequences in B. subtilis, indicating that B. subtilis secretes some heterologous proteins via an unknown pathway. CONCLUSIONS Small laccases from S. coelicolor, S. viridosporus and Amycolatopsis 75iv2 were secreted in both Gram-positive expression hosts B. subtilis and S. lividans, but the extracellular activities were significantly higher in the latter.
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Affiliation(s)
- Silja Välimets
- Department of Food Sciences and Technology, University of Natural Resources and Life Sciences, Institute of Food Technology, Muthgasse 18, Vienna, Vienna, 1190, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Vienna, 1190, Austria
| | - Patricia Pedetti
- Food Microbiology, Wageningen University and Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, The Netherlands
| | - Ludovika Jessica Virginia
- Department of Food Sciences and Technology, University of Natural Resources and Life Sciences, Institute of Food Technology, Muthgasse 18, Vienna, Vienna, 1190, Austria
| | - Mai Ngoc Hoang
- Department of Food Sciences and Technology, University of Natural Resources and Life Sciences, Institute of Food Technology, Muthgasse 18, Vienna, Vienna, 1190, Austria
- Department of Human Medicine, Institute of Immunology, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129, Oldenburg, Germany
| | - Michael Sauer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Vienna, 1190, Austria
| | - Clemens Peterbauer
- Department of Food Sciences and Technology, University of Natural Resources and Life Sciences, Institute of Food Technology, Muthgasse 18, Vienna, Vienna, 1190, Austria.
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7
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He B, Sachla AJ, Helmann JD. TerC Proteins Function During Protein Secretion to Metalate Exoenzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536223. [PMID: 37090602 PMCID: PMC10120614 DOI: 10.1101/2023.04.10.536223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Cytosolic metalloenzymes acquire metals from buffered intracellular pools. How exported metalloenzymes are appropriately metalated is less clear. We provide evidence that TerC family proteins function in metalation of enzymes during export through the general secretion (Sec-dependent) pathway. Bacillus subtilis strains lacking MeeF(YceF) and MeeY(YkoY) have a reduced capacity for protein export and a greatly reduced level of manganese (Mn) in the secreted proteome. MeeF and MeeY copurify with proteins of the general secretory pathway, and in their absence the FtsH membrane protease is essential for viability. MeeF and MeeY are also required for efficient function of the Mn 2+ -dependent lipoteichoic acid synthase (LtaS), a membrane-localized enzyme with an extracytoplasmic active site. Thus, MeeF and MeeY, representative of the widely conserved TerC family of membrane transporters, function in the co-translocational metalation of Mn 2+ -dependent membrane and extracellular enzymes.
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Affiliation(s)
- Bixi He
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
| | - Ankita J. Sachla
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
| | - John D. Helmann
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
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8
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D’aes J, Fraiture MA, Bogaerts B, De Keersmaecker SCJ, Roosens NHCJ, Vanneste K. Metagenomic Characterization of Multiple Genetically Modified Bacillus Contaminations in Commercial Microbial Fermentation Products. LIFE (BASEL, SWITZERLAND) 2022; 12:life12121971. [PMID: 36556336 PMCID: PMC9781105 DOI: 10.3390/life12121971] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
Genetically modified microorganisms (GMM) are frequently employed for manufacturing microbial fermentation products such as food enzymes or vitamins. Although the fermentation product is required to be pure, GMM contaminations have repeatedly been reported in numerous commercial microbial fermentation produce types, leading to several rapid alerts at the European level. The aim of this study was to investigate the added value of shotgun metagenomic high-throughput sequencing to confirm and extend the results of classical analysis methods for the genomic characterization of unauthorized GMM. By combining short- and long-read metagenomic sequencing, two transgenic constructs were characterized, with insertions of alpha-amylase genes originating from B. amyloliquefaciens and B. licheniformis, respectively, and a transgenic construct with a protease gene insertion originating from B. velezensis, which were all present in all four investigated samples. Additionally, the samples were contaminated with up to three unculturable Bacillus strains, carrying genetic modifications that may hamper their ability to sporulate. Moreover, several samples contained viable Bacillus strains. Altogether these contaminations constitute a considerable load of antimicrobial resistance genes, that may represent a potential public health risk. In conclusion, our study showcases the added value of metagenomics to investigate the quality and safety of complex commercial microbial fermentation products.
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9
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First echinoderm alpha-amylase from a tropical sea cucumber (Holothuria leucospilota): Molecular cloning, tissue distribution, cellular localization and functional production in a heterogenous E.coli system with codon optimization. PLoS One 2020; 15:e0239044. [PMID: 32931501 PMCID: PMC7491741 DOI: 10.1371/journal.pone.0239044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/28/2020] [Indexed: 11/19/2022] Open
Abstract
Holothuria leucospilota (Echinodermata: Holothuroidea) is a widespread tropical sea cucumber with strong value for the ecological restoration of coral reefs. Therefore, some studies regarding the artificial breeding and cultivation of H. leucospilota have been undertaken recently. However, the biological functions of the digestive system of this species have not been elucidated. In this study, a cDNA coding for α-amylase, an indicator of digestive maturity in animals, was identified from H. leucospilota and designated Hl-Amy. The full-length cDNA of the Hl-Amy gene, which is 1734 bp in length with an open reading frame (ORF) of 1578 bp, encodes a 525 amino acid (a.a.) protein with a deduced molecular weight of 59.34 kDa. According to the CaZy database annotation, Hl-Amy belongs to the class of GH-H with the official nomenclature of α-amylase (EC 3.2.1.1) or 4-α-D-glucan glucanohydrolase. The Hl-Amy protein contains a signal peptide at the N-terminal followed by a functional amylase domain, which includes the catalytic activity site. The mRNA expression of Hl-Amy was abundantly exhibited in the intestine, followed by the transverse vessel with a low level, but was hardly detected in other selected tissues. During embryonic and larval development, Hl-Amy was constitutively expressed in all stages, and the highest expression level was observed in the blastula. By in situ hybridization (ISH), positive Hl-Amy signals were observed in different parts of the three different intestinal segments (foregut, midgut and hindgut). The Hl-Amy recombinant protein was generated in an E. coli system with codon optimization, which is necessary for Hl-Amy successfully expressed in this heterogenous system. The Hl-Amy recombinant protein was purified by immobilized metal ion affinity chromatography (IMAC), and its activity of starch hydrolysis was further detected. The optimal temperatures and pH for Hl-Amy recombinant protein were 55°C and 6.0, respectively, with an activity of 62.2 U/mg. In summary, this current study has filled a knowledge gap on the biological function and expression profiles of an essential digestive enzyme in sea cucumber, which may encourage future investigation toward rationalized diets for H. leucospilota in artificial cultivation, and optimized heterogenous prokaryotic systems for producing recombinant enzymes of marine origins.
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10
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Mohseni AH, Taghinezhad-Saroukalaei S, Voglmeir J. Recombinant Glycoenzyme Production in Gram-Positive Bacteria—An Overview. TRENDS GLYCOSCI GLYC 2020. [DOI: 10.4052/tigg.1824.1e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Amir Hossein Mohseni
- Glycomics and Glycan Bioengineering Research Center, Nanjing Agricultural University
- Department of Microbiology, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University
| | - Sedigheh Taghinezhad-Saroukalaei
- Glycomics and Glycan Bioengineering Research Center, Nanjing Agricultural University
- Department of Microbiology, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center, Nanjing Agricultural University
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11
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Sharma A, Gupta G, Ahmad T, Mansoor S, Kaur B. Enzyme Engineering: Current Trends and Future Perspectives. FOOD REVIEWS INTERNATIONAL 2019. [DOI: 10.1080/87559129.2019.1695835] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Anshula Sharma
- Department of Biotechnology, Punjabi University, Patiala, India
| | - Gaganjot Gupta
- Department of Biotechnology, Punjabi University, Patiala, India
| | - Tawseef Ahmad
- Department of Biotechnology, Punjabi University, Patiala, India
| | | | - Baljinder Kaur
- Department of Biotechnology, Punjabi University, Patiala, India
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12
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Hu X, Lai CYN, Sivakumar T, Wang H, Ng KL, Lam CC, Wong WKR. Novel strategy for expression of authentic and bioactive human basic fibroblast growth factor in Bacillus subtilis. Appl Microbiol Biotechnol 2018; 102:7061-7069. [PMID: 29951857 DOI: 10.1007/s00253-018-9176-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 12/20/2022]
Abstract
Inteins, also known as "protein introns," have been found to be present in many microbial species and widely employed for the expression and purification of recombinant proteins in Escherichia coli. However, interestingly, until now there has not been much information on the identification and application of inteins to protein expression in Bacillus subtilis. In this article, for the first time, despite the likelihood of absence of inteins in B. subtilis, this bacterium was shown to be able to facilitate auto-catalytic cleavages of fusions formed between inteins and recombinant proteins. Employing a construct expressing the intein, Ssp DnaB, (DnaB), which was fused at its N-terminus with the cellulose-binding domain (CellBD) of an endoglucanase encoded by the cenA gene of Cellulomonas fimi, the construct was demonstrated to be capable of mediating intracellular expression of basic fibroblast growth factor (bFGF), followed by auto-processing of the CellBD-DnaB-bFGF fusion to result in bFGF possessing the 146-residue authentic structure. The mentioned fusion was shown to result in a high yield of 84 mg l-1 of biologically active bFGF. Future work in improving the growth of B. subtilis may enable the use of this bacterium, working in cooperation with inteins, to result in a new platform for efficient expression of valuable proteins.
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Affiliation(s)
- Xiuhua Hu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Cheuk Yin Nelson Lai
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - T Sivakumar
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Hao Wang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - K L Ng
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - C C Lam
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - W K R Wong
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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13
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Perera VR, Lapek JD, Newton GL, Gonzalez DJ, Pogliano K. Identification of the S-transferase like superfamily bacillithiol transferases encoded by Bacillus subtilis. PLoS One 2018; 13:e0192977. [PMID: 29451913 PMCID: PMC5815605 DOI: 10.1371/journal.pone.0192977] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/01/2018] [Indexed: 11/18/2022] Open
Abstract
Bacillithiol is a low molecular weight thiol found in Firmicutes that is analogous to glutathione, which is absent in these bacteria. Bacillithiol transferases catalyze the transfer of bacillithiol to various substrates. The S-transferase-like (STL) superfamily contains over 30,000 putative members, including bacillithiol transferases. Proteins in this family are extremely divergent and are related by structural rather than sequence similarity, leaving it unclear if all share the same biochemical activity. Bacillus subtilis encodes eight predicted STL superfamily members, only one of which has been shown to be a bacillithiol transferase. Here we find that the seven remaining proteins show varying levels of metal dependent bacillithiol transferase activity. We have renamed the eight enzymes BstA-H. Mass spectrometry and gene expression studies revealed that all of the enzymes are produced to varying levels during growth and sporulation, with BstB and BstE being the most abundant and BstF and BstH being the least abundant. Interestingly, several bacillithiol transferases are induced in the mother cell during sporulation. A strain lacking all eight bacillithiol transferases showed normal growth in the presence of stressors that adversely affect growth of bacillithiol-deficient strains, such as paraquat and CdCl2. Thus, the STL bacillithiol transferases represent a new group of proteins that play currently unknown, but potentially significant roles in bacillithiol-dependent reactions. We conclude that these enzymes are highly divergent, perhaps to cope with an equally diverse array of endogenous or exogenous toxic metabolites and oxidants.
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Affiliation(s)
- Varahenage R. Perera
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States of America
| | - John D. Lapek
- Department of Pharmacology and Pharmacy, School of Medicine, University of California, San Diego, La Jolla, CA, United States of America
| | - Gerald L. Newton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States of America
| | - David J. Gonzalez
- Department of Pharmacology and Pharmacy, School of Medicine, University of California, San Diego, La Jolla, CA, United States of America
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States of America
- * E-mail:
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14
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Abstract
One of the greatest sources of metabolic and enzymatic diversity are microorganisms. In recent years, emerging recombinant DNA and genomic techniques have facilitated the development of new efficient expression systems, modification of biosynthetic pathways leading to new metabolites by metabolic engineering, and enhancement of catalytic properties of enzymes by directed evolution. Complete sequencing of industrially important microbial genomes is taking place very rapidly, and there are already hundreds of genomes sequenced. Functional genomics and proteomics are major tools used in the search for new molecules and development of higher-producing strains.
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Affiliation(s)
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CDMX, México
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Sushma C, Anand AP, Veeranki VD. Enhanced production of glutaminase free L-asparaginase II by Bacillus subtilis WB800N through media optimization. KOREAN J CHEM ENG 2017. [DOI: 10.1007/s11814-017-0211-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Yan S, Wu G. Bottleneck in secretion of α-amylase in Bacillus subtilis. Microb Cell Fact 2017; 16:124. [PMID: 28724440 PMCID: PMC5518135 DOI: 10.1186/s12934-017-0738-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/10/2017] [Indexed: 11/10/2022] Open
Abstract
Amylase plays an important role in biotechnology industries, and Gram-positive bacterium Bacillus subtilis is a major host to produce heterogeneous α-amylases. However, the secretion stress limits the high yield of α-amylase in B. subtilis although huge efforts have been made to address this secretion bottleneck. In this question-oriented review, every effort is made to answer the following questions, which look simple but are long-standing, through reviewing of literature: (1) Does α-amylase need a specific and dedicated chaperone? (2) What signal sequence does CsaA recognize? (3) Does CsaA require ATP for its operation? (4) Does an unfolded α-amylase is less soluble than a folded one? (5) Does α-amylase aggregate before transporting through Sec secretion system? (6) Is α-amylase sufficient stable to prevent itself from misfolding? (7) Does α-amylase need more disulfide bonds to be stabilized? (8) Which secretion system does PrsA pass through? (9) Is PrsA ATP-dependent? (10) Is PrsA reused after folding of α-amylase? (11) What is the fate of PrsA? (12) Is trigger factor (TF) ATP-dependent? The literature review suggests that not only the most of those questions are still open to answers but also it is necessary to calculate ATP budget in order to better understand how B. subtilis uses its energy for production and secretion.
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Affiliation(s)
- Shaomin Yan
- National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China
| | - Guang Wu
- National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China.
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17
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Poly-γ-glutamic acid productivity of Bacillus subtilis BsE1 has positive function in motility and biocontrol against Fusarium graminearum. J Microbiol 2017; 55:554-560. [PMID: 28664519 DOI: 10.1007/s12275-017-6589-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/05/2017] [Accepted: 04/18/2017] [Indexed: 10/19/2022]
Abstract
In this study, we investigate the relationship between γ-PGA productivity and biocontrol capacity of Bacillus subtilis BsE1; one bacterial isolate displayed 62.14% biocontrol efficacy against Fusarium root rot. The γ-PGA yield assay, motility assay, wheat root colonization assay, and biological control assay were analysed in different γ-PGA yield mutants of BsE1. The pgsB (PGA-synthase-CapB gene) deleted mutant of BsE1 reduced γ-PGA yield and exhibited apparent decline of in vitro motile ability. Deletion of pgsB impaired colonizing capacity of BsE1 on wheat root in 30 days, also lowered biocontrol efficacies from 62.08% (wild type BsE1) to 14.22% in greenhouse experiment against Fusarium root rot. The knockout of pgdS and ggt (genes relate to two γ-PGA degrading enzymes) on BsE1, leads to a considerable improvement in polymer yield and biocontrol efficacy, which attains higher level compared with wild type BsE1. Compared with ΔpgsB mutant, defense genes related to reactive oxygen species (ROS) and phytoalexin expressed changes by notable levels on wheat roots treated with BsE1, demonstrating the functional role γ-PGA plays in biocontrol against Fusarium root rot. γ-PGA is not only important to the motile and plant root colonization ability of BsE1, but also essential to the biological control performed by BsE1 against Fusarium root rot. Our goal in this study is to reveals a new perspective of BCAs screening on bacterial isolates, without good performance during pre-assays of antagonism ability.
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Neef J, Bongiorni C, Goosens VJ, Schmidt B, van Dijl JM. Intramembrane protease RasP boosts protein production in Bacillus. Microb Cell Fact 2017; 16:57. [PMID: 28376795 PMCID: PMC5381017 DOI: 10.1186/s12934-017-0673-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 03/31/2017] [Indexed: 11/10/2022] Open
Abstract
Background The microbial cell factory Bacillus subtilis is a popular industrial platform for high-level production of secreted technical enzymes. Nonetheless, the effective secretion of particular heterologous enzymes remains challenging. Over the past decades various studies have tackled this problem, and major improvements were achieved by optimizing signal peptides or removing proteases involved in product degradation. On the other hand, serious bottlenecks in the protein export process per se remained enigmatic, especially for protein secretion at commercially significant levels by cells grown to high density. The aim of our present study was to assess the relevance of the intramembrane protease RasP for high-level protein production in B. subtilis. Results Deletion of the rasP gene resulted in reduced precursor processing and extracellular levels of the overproduced α-amylases AmyE from B. subtilis and AmyL from Bacillus licheniformis. Further, secretion of the overproduced serine protease BPN’ from Bacillus amyloliquefaciens was severely impaired in the absence of RasP. Importantly, overexpression of rasP resulted in threefold increased production of a serine protease from Bacillus clausii, and 2.5- to 10-fold increased production of an AmyAc α-amylase from Paenibacillus curdlanolyticus, depending on the culture conditions. Of note, growth defects due to overproduction of the two latter enzymes were suppressed by rasP-overexpression. Conclusion Here we show that an intramembrane protease, RasP, sets a limit to high-level production of two secreted heterologous enzymes that are difficult to produce in the B. subtilis cell factory. This finding was unexpected and suggests that proteolytic membrane sanitation is key to effective enzyme production in Bacillus.
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Affiliation(s)
- Jolanda Neef
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Cristina Bongiorni
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA, 94304, USA
| | - Vivianne J Goosens
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.,Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Brian Schmidt
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA, 94304, USA
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.
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19
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Lee S, Katya K, Park Y, Won S, Seong M, Hamidoghli A, Bai SC. Comparative evaluation of dietary probiotics Bacillus subtilis WB60 and Lactobacillus plantarum KCTC3928 on the growth performance, immunological parameters, gut morphology and disease resistance in Japanese eel, Anguilla japonica. FISH & SHELLFISH IMMUNOLOGY 2017; 61:201-210. [PMID: 28034835 DOI: 10.1016/j.fsi.2016.12.035] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/23/2016] [Accepted: 12/24/2016] [Indexed: 06/06/2023]
Abstract
The current experiment was conducted to evaluate and compare the efficacy of two different probiotics Bacillus subtilis WB60 and Lactobacillus plantarum KCTC3928 in diet of Japanese eel, Anguilla japonica. Seven experimental diets were formulated to contain no probiotics (CON), three graded levels of B. subtilis at 106 (BS1), 107 (BS2), 108 (BS3) and L. plantarum at 106 (LP1), 107 (LP2), 108 (LP3) CFU/g diet. Twenty fish averaging 8.29 ± 0.06 g were distributed in to 21 aquaria and were randomly assigned to one of the experimental diets in triplicate groups. Average weight gain (WG), feed efficiency (FE), and protein efficiency ratio (PER) of fish fed B. subtilis at 107 (BS2) and 108 (BS3) CFU/g diet were significantly higher than those of fish fed other experimental diets (P < 0.05). Nonspecific enzymatic activities including lysozyme, superoxide dismutase (SOD), myeloperoxidase (MPO) from fish fed B. subtilis at 107 (BS2) and 108 (BS3) CFU/g diet were detected to be significantly higher than that from fish fed CON diet (P < 0.05). Whereas, level of intestine glyceraldehyde-3-phosphate dehydrogenase (GAPDH), heat shock protein 70, 90 (HSP70, 90) and immunoglobulin (IgM) from fish fed B. subtilis at 107 and 108 CFU/g diet were recorded to be significantly higher than those of fish fed other experimental diets (P < 0.05). Parameters for intestinal morphology and histology suggested a healthier gut for the fish fed108 (BS3) CFU/g diet as compared to other treatment groups. Whereas, results from the disease challenge test with bacteria Vibrio angulillarum showed significantly lower survival rate for fish fed CON diet than those of fish fed other experimental diets. Therefore, these results indicated that oral supplement of B. subtilis at 108 (BS3) CFU/g diet could be a more effective source of probiotic compared to L. plantarum in Japanese eel.
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Affiliation(s)
- Seunghan Lee
- Dept. of Marine Bio-materials and Aquaculture/Feeds & Foods Nutrition Research Center (FFNRC), Pukyong National University, Busan, 608-737, Republic of Korea
| | | | - Youngjin Park
- Dept. of Marine Bio-materials and Aquaculture/Feeds & Foods Nutrition Research Center (FFNRC), Pukyong National University, Busan, 608-737, Republic of Korea
| | - Seonghun Won
- Dept. of Marine Bio-materials and Aquaculture/Feeds & Foods Nutrition Research Center (FFNRC), Pukyong National University, Busan, 608-737, Republic of Korea
| | - Minji Seong
- Dept. of Marine Bio-materials and Aquaculture/Feeds & Foods Nutrition Research Center (FFNRC), Pukyong National University, Busan, 608-737, Republic of Korea
| | - Ali Hamidoghli
- Dept. of Marine Bio-materials and Aquaculture/Feeds & Foods Nutrition Research Center (FFNRC), Pukyong National University, Busan, 608-737, Republic of Korea
| | - Sungchul C Bai
- Dept. of Marine Bio-materials and Aquaculture/Feeds & Foods Nutrition Research Center (FFNRC), Pukyong National University, Busan, 608-737, Republic of Korea.
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20
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Ploss TN, Reilman E, Monteferrante CG, Denham EL, Piersma S, Lingner A, Vehmaanperä J, Lorenz P, van Dijl JM. Homogeneity and heterogeneity in amylase production by Bacillus subtilis under different growth conditions. Microb Cell Fact 2016; 15:57. [PMID: 27026185 PMCID: PMC4812647 DOI: 10.1186/s12934-016-0455-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/22/2016] [Indexed: 12/22/2022] Open
Abstract
Background Bacillus subtilis is an important cell factory for the biotechnological industry due to its ability to secrete commercially relevant proteins in large amounts directly into the growth medium. However, hyper-secretion of proteins, such as α-amylases, leads to induction of the secretion stress-responsive CssR-CssS regulatory system, resulting in up-regulation of the HtrA and HtrB proteases. These proteases degrade misfolded proteins secreted via the Sec pathway, resulting in a loss of product. The aim of this study was to investigate the secretion stress response in B. subtilis 168 cells overproducing the industrially relevant α-amylase AmyM from Geobacillus stearothermophilus, which was expressed from the strong promoter P(amyQ)-M. Results Here we show that activity of the htrB promoter as induced by overproduction of AmyM was “noisy”, which is indicative for heterogeneous activation of the secretion stress pathway. Plasmids were constructed to allow real-time analysis of P(amyQ)-M promoter activity and AmyM production by, respectively, transcriptional and out-of-frame translationally coupled fusions with gfpmut3. Our results show the emergence of distinct sub-populations of high- and low-level AmyM-producing cells, reflecting heterogeneity in the activity of P(amyQ)-M. This most likely explains the heterogeneous secretion stress response. Importantly, more homogenous cell populations with regard to P(amyQ)-M activity were observed for the B. subtilis mutant strain 168degUhy32, and the wild-type strain 168 under optimized growth conditions. Conclusion Expression heterogeneity of secretory proteins in B. subtilis can be suppressed by degU mutation and optimized growth conditions. Further, the out-of-frame translational fusion of a gene for a secreted target protein and gfp represents a versatile tool for real-time monitoring of protein production and opens novel avenues for Bacillus production strain improvement.
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Affiliation(s)
- Tina N Ploss
- AB Enzymes GmbH, Feldbergstrasse 78, 64293, Darmstadt, Germany
| | - Ewoud Reilman
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RD, Groningen, The Netherlands
| | - Carmine G Monteferrante
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RD, Groningen, The Netherlands.,Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Emma L Denham
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RD, Groningen, The Netherlands.,Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Sjouke Piersma
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RD, Groningen, The Netherlands
| | - Anja Lingner
- AB Enzymes GmbH, Feldbergstrasse 78, 64293, Darmstadt, Germany.,c-LEcta GmbH, Perlickstraße 5, 04103, Leipzig, Germany
| | | | - Patrick Lorenz
- AB Enzymes GmbH, Feldbergstrasse 78, 64293, Darmstadt, Germany
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RD, Groningen, The Netherlands.
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21
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Optimization of the secretion pathway for heterologous proteins in Bacillus subtilis. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0843-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Cai L, Indrakumar S, Kiarie E, Kim IH. Effects of a multi-strain Bacillus species-based direct-fed microbial on growth performance, nutrient digestibility, blood profile, and gut health in nursery pigs fed corn-soybean meal-based diets. J Anim Sci 2015; 93:4336-42. [PMID: 26440333 DOI: 10.2527/jas.2015-9056] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
This experiment was conducted to investigate the effect of a spp.-based direct-fed microbial (DFM) on growth performance, apparent total tract digestibility (ATTD), blood profile, intestinal histomorphology, and fecal gas emission in piglets fed corn and soybean meal-based diets. The DFM product was based on 1 strain of and 2 strains of and formulated to supply 1.5 × 10 cfu/g of feed. A total of 128 piglets ([Yorkshire × Landrace] × Duroc; 6.8 ± 0.6 kg BW; weaning age: 24 d) were housed in groups (4 pigs/pen, 2 barrows and 2 gilts) and fed diets ( = 16) without or with DFM in a 2-phase feeding program: d 0 to 14 (phase I) and 15 to 42 (phase II). Feed intake and BW were measured weekly. At the end of each phase, samples for blood urea nitrogen (BUN), blood creatinine, ATTD, and fecal noxious gas emission were taken. At termination, 12 piglets per treatment were killed to access intestinal tissues for histomorphology. Overall, pigs fed DFM had a greater ( < 0.05) G:F than pigs fed the control diet. In phase I, pigs fed DFM showed a greater ( < 0.05) ADG and lower ( < 0.05) concentration of BUN and fecal ammonia emission than the control group. In phase II, a greater ( < 0.05) ATTD of nitrogen and longer ( < 0.05) duodenum and jejunum villi were observed in pigs fed the DFM diet compared with the control group. In conclusion, inclusion of DFM improved growth performance and villi length of the duodenum and jejunum in nursery pigs. Furthermore, DFM enhanced protein utilization as demonstrated by increased nitrogen digestibility, lower BUN, and lower fecal ammonia release.
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23
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Goswami A, Roy Chowdhury A, Sarkar M, Saha SK, Paul S, Dutta C. Strand-biased gene distribution, purine assymetry and environmental factors influence protein evolution in Bacillus. FEBS Lett 2015; 589:629-38. [PMID: 25639611 DOI: 10.1016/j.febslet.2015.01.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/16/2015] [Accepted: 01/18/2015] [Indexed: 12/23/2022]
Abstract
A strong purine asymmetry, along with strand-biased gene distribution and the presence of PolC, prevails in Bacillus and some other members of Firmicutes, Fusobacteria and Tenericutes. The analysis of protein features in 21 Bacillus species of diverse metabolic, virulence and ecological traits revealed that purine asymmetry in conjunction with lineage/niche specific constraints significantly influences protein evolution in Bacillus. All Bacillus species, except for Se-respiring Bacillus selenitireducens, display distinct strand-specific biases in amino acid usage, which may affect the isoelectric point or surface charge distribution of proteins with prevalence of acidic and basic residues in the leading and lagging strand proteins, respectively.
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Affiliation(s)
- Aranyak Goswami
- Structural Biology & Bioinformatics Division, CSIR - Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India.
| | - Anindya Roy Chowdhury
- Structural Biology & Bioinformatics Division, CSIR - Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India.
| | - Munmun Sarkar
- Structural Biology & Bioinformatics Division, CSIR - Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India.
| | - Sanjoy Kumar Saha
- Structural Biology & Bioinformatics Division, CSIR - Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India.
| | - Sandip Paul
- Structural Biology & Bioinformatics Division, CSIR - Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India.
| | - Chitra Dutta
- Structural Biology & Bioinformatics Division, CSIR - Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India.
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24
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Toya Y, Hirasawa T, Morimoto T, Masuda K, Kageyama Y, Ozaki K, Ogasawara N, Shimizu H. 13C-metabolic flux analysis in heterologous cellulase production by Bacillus subtilis genome-reduced strain. J Biotechnol 2014; 179:42-9. [DOI: 10.1016/j.jbiotec.2014.03.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 02/14/2014] [Accepted: 03/14/2014] [Indexed: 01/19/2023]
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25
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Nguyen QA, Schumann W. Use of IPTG-inducible promoters for anchoring recombinant proteins on the Bacillus subtilis spore surface. Protein Expr Purif 2013; 95:67-76. [PMID: 24326192 DOI: 10.1016/j.pep.2013.11.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 11/24/2013] [Accepted: 11/27/2013] [Indexed: 02/06/2023]
Abstract
The method of surface display allows the fusion of passenger proteins to a carrier protein displayed on the outside of bioparticles such as spores. Here, we used spores of Bacillus subtilis, the outer surface proteins CotB, CotC, and CotG as carrier and the amyQ-encoded α-amylase and GFPuv as passenger proteins. The different translational fusions were fused to two different IPTG-inducible promoters, and the regulated expression level of both passenger proteins were measured in relation to the inducer concentration added to sporulating cells. It turned out that the amount of fusion protein on the outside of spores was dependent on the amount of IPTG added, but the optimal amount of inducer varied depending on the carrier and the passenger proteins. These experiments demonstrate that a regulatable expression of passenger proteins on the surface of spores is possible. This will help to adjust the amount of any passenger protein to that needed for specific purposes.
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Affiliation(s)
- Quynh Anh Nguyen
- Department of Molecular and Environmental Biotechnology, Faculty of Biology, University of Science, Vietnam National University, HCMC, Viet Nam
| | - Wolfgang Schumann
- Institute of Genetics, University of Bayreuth, D-95440 Bayreuth, Germany.
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26
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Mulder KC, Bandola J, Schumann W. Construction of an artificial secYEG operon allowing high level secretion of α-amylase. Protein Expr Purif 2013; 89:92-6. [DOI: 10.1016/j.pep.2013.02.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 02/04/2013] [Accepted: 02/06/2013] [Indexed: 10/27/2022]
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27
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Ying Q, Zhang C, Guo F, Wang S, Bie X, Lu F, Lu Z. Secreted Expression of a Hyperthermophilic α-Amylase Gene from Thermococcus sp. HJ21 in Bacillus subtilis. J Mol Microbiol Biotechnol 2013; 22:392-8. [DOI: 10.1159/000346215] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Abstract
Microorganisms are one of the greatest sources of metabolic and enzymatic diversity. In recent years, emerging recombinant DNA and genomic techniques have facilitated the development of new efficient expression systems, modification of biosynthetic pathways leading to new metabolites by metabolic engineering, and enhancement of catalytic properties of enzymes by directed evolution. Complete sequencing of industrially important microbial genomes is taking place very rapidly and there are already hundreds of genomes sequenced. Functional genomics and proteomics are major tools used in the search for new molecules and development of higher-producing strains.
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Jabbour D, Sorger A, Sahm K, Antranikian G. A highly thermoactive and salt-tolerant α-amylase isolated from a pilot-plant biogas reactor. Appl Microbiol Biotechnol 2012; 97:2971-8. [PMID: 22743714 PMCID: PMC3602641 DOI: 10.1007/s00253-012-4194-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 05/16/2012] [Accepted: 05/17/2012] [Indexed: 11/25/2022]
Abstract
Aiming at the isolation of novel enzymes from previously uncultured thermophilic microorganisms, a metagenome library was constructed from DNA isolated from a pilot-plant biogas reactor operating at 55 °C. The library was screened for starch-degrading enzymes, and one active clone was found. An open reading frame of 1,461 bp encoding an α-amylase from an uncultured organism was identified. The amy13A gene was cloned in Escherichia coli, resulting in high-level expression of the recombinant amylase. The novel enzyme Amy13A showed the highest sequence identity (75%) to α-amylases from Petrotoga mobilis and Halothermothrix orenii. Amy13A is highly thermoactive, exhibiting optimal activity at 80 °C, and it is also highly salt-tolerant, being active in 25% (w/v) NaCl. Amy13A is one of the few enzymes that tolerate high concentrations of salt and elevated temperatures, making it a potential candidate for starch processing under extreme conditions.
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Affiliation(s)
- Dina Jabbour
- Institute of Technical Microbiology, Hamburg University of Technology, Kasernenstr. 12, Hamburg, 21073, Germany.
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Signal perception by the secretion stress-responsive CssRS two-component system in Bacillus subtilis. J Bacteriol 2012; 194:1800-14. [PMID: 22307758 DOI: 10.1128/jb.05767-11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The CssRS two-component system responds to heat and secretion stresses in Bacillus subtilis by controlling expression of HtrA and HtrB chaperone-type proteases and positively autoregulating its own expression. Here we report on the features of the CssS extracellular loop domain that are involved in signal perception and on CssS subcellular localization. Individual regions of the CssS extracellular loop domain contribute differently to signal perception and activation. The conserved hydrophilic 26-amino-acid segment juxtaposed to transmembrane helix 1 is involved in the switch between the deactivated and activated states, while the conserved 19-amino-acid hydrophobic segment juxtaposed to transmembrane 2 is required for signal perception and/or transduction. Perturbing the size of the extracellular loop domain increases CssS kinase activity and makes it unresponsive to secretion stress. CssS is localized primarily at the septum but is also found in a punctate pattern with lower intensity throughout the cell cylinder. Moreover, the CssRS-controlled HtrA and HtrB proteases are randomly distributed in foci throughout the cell surface, with more HtrB than HtrA foci in unstressed cells.
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Analysis and application of Bacillus subtilis sortases to anchor recombinant proteins on the cell wall. AMB Express 2011; 1:22. [PMID: 21906378 PMCID: PMC3222306 DOI: 10.1186/2191-0855-1-22] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 07/21/2011] [Indexed: 02/06/2023] Open
Abstract
Bacillus subtilis codes for two putative sortases, YhcS and YwpE, and two surface proteins, YhcR and YfkN, harboring sorting motifs supposed to be recognized by the putative sortase(s). However, there is no experimental evidence to show a direct link between these sortases and sorting sequences. To study the role of these two putative sortases on displaying YhcR and YfkN on the cell wall, expression of yhcS and ywpE was analyzed by transcriptional fusions and by Northern blot. It turned out that yhcS gene is expressed at a higher level during the late stationary phase from both experiments, while ywpE expression is not confirmed in the Northern blot analysis. Next, we constructed yhcS and ywpE single and double knockout strains and plasmids that express one or both genes to restore the functions of the knockout strains. It could be shown that display of YhcR and YfkN on the surface depended on the presence of YhcS while YwpE seems not to play a major role if any as a sortase. Finally, the putative sorting motif together with a 123-amino-acid spacer derived from YhcR and YfkN designated YhcR123 and YfkN123, respectively, were fused to an α-amylase reporter enzyme. The fusion protein YhcR123-AmyQ could be displayed on the surface at high amounts, while YfkN123-AmyQ could be hardly detected. We conclude that the sortase YhcS can recognize and anchor YhcR on the cell wall. This result further indicates that the YhcR sorting sequence can be used to display recombinant proteins on the surface of B. subtilis cells.
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Rabbani M, Mirmohammad Sadeghi H, Moazen F, Rahimi M, Salehi G. Cloning and Expression of Randomly Mutated Bacillus subtilis α-Amylase Genes in HB101. BIOTECHNOLOGY RESEARCH INTERNATIONAL 2011; 2011:305956. [PMID: 21808739 PMCID: PMC3145346 DOI: 10.4061/2011/305956] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 05/26/2011] [Indexed: 11/30/2022]
Abstract
The aim of this study was to isolate and express the randomly mutated
α-amylase gene from B.
subtilis strain 168. BS168F:
5′-gtgtcaagaatgtttgc-3′
and BS168R:
3′-gttttgttaaaagatga-5′
primers were used to amplify the amylase gene using the following
cycle in error-prone PCR method: 94°C for
30 s, 40°C for 2 min, and
72°C for 2 min in 30 cycles that were
followed with 72°C for 2 min as a post cycle.
E. coli XL1 blue was used as host for plasmid
construction. Amylase enzyme activity assay was performed using
continuous spectrophotometric procedures. Results of sequencing showed
that sequence was cloned from the first ATG and with the correct open
reading frame. Having confirmed the integrity of the insert, the gene
was ligated into expression vector pET-15b and then further confirmed
using digestion analysis. Amylase activity showed 3 clones with higher
enzymatic activity compared with the wild type. Error-prone PCR method
produced a mutated gene that provides amylase activity much higher
than that of wild type. Sequencing the mutated genes should shed light
on the important region of the genes that could be manipulated in
future studies.
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Affiliation(s)
- Mohammed Rabbani
- Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Centre, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
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Trip H, van der Veek PJ, Renniers TC, Meima R, Sagt CM, Mohrmann L, Kuipers OP. A novel screening system for secretion of heterologous proteins in Bacillus subtilis. Microb Biotechnol 2011; 4:673-82. [PMID: 21624103 PMCID: PMC3819016 DOI: 10.1111/j.1751-7915.2011.00270.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
High‐level production of secretory proteins in Bacillus subtilis leads to a stress response involving the two‐component system CssRS and its target genes htrA and htrB. Here, we used this sensing system in a reporter strain in which gfp is under control of PhtrA, the secretion stress responsive promoter of htrA. Overexpression of heterologous secretory proteins in this strain results in green fluorescent cells, which can be separated from non‐secreting, low fluorescent cells using a fluorescence‐activated cell sorter (FACS). Using this principle, genomic libraries of uncharacterized prokaryotic organisms, expressed in the reporter strain, can be screened for genes encoding secretory proteins.
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Affiliation(s)
- Hein Trip
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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Role of the cell wall microenvironment in expression of a heterologous SpaP-S1 fusion protein by Streptococcus gordonii. Appl Environ Microbiol 2010; 77:1660-6. [PMID: 21193663 DOI: 10.1128/aem.02178-10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The charge density in the cell wall microenvironment of Gram-positive bacteria is believed to influence the expression of heterologous proteins. To test this, the expression of a SpaP-S1 fusion protein, consisting of the surface protein SpaP of Streptococcus mutans and a pertussis toxin S1 fragment, was studied in the live vaccine candidate bacterium Streptococcus gordonii. Results showed that the parent strain PM14 expressed very low levels of SpaP-S1. By comparison, the dlt mutant strain, which has a mutation in the dlt operon preventing d-alanylation of the cell wall lipoteichoic acids, and another mutant strain, OB219(pPM14), which lacks the LPXTG major surface proteins SspA and SspB, expressed more SpaP-S1 than the parent. Both the dlt mutant and the OB219(pPM14) strain had a more negatively charged cell surface than PM14, suggesting that the negative charged cell wall played a role in the increase in SpaP-S1 production. Accordingly, the addition of Ca(2+), Mg(2+), and K(+), presumably increasing the positive charge of the cell wall, led to a reduction in SpaP-S1 production, while the addition of bicarbonate resulted in an increase in SpaP-S1 production. The level of SpaP-S1 production could be correlated with the level of PrsA, a peptidyl-prolyl cis/trans isomerase, in the cells. PrsA expression appears to be regulated by the cell envelope stress two-component regulatory system LiaSR. The results collectively indicate that the charge density of the cell wall microenvironment can modulate heterologous SpaP-S1 protein expression in S. gordonii and that this modulation is mediated by the level of PrsA, whose expression is regulated by the LiaSR two-component regulatory system.
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35
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Contributions of the pre- and pro-regions of a Staphylococcus hyicus lipase to secretion of a heterologous protein by Bacillus subtilis. Appl Environ Microbiol 2009; 76:659-69. [PMID: 19948853 DOI: 10.1128/aem.01671-09] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis is a well-established cell factory for efficient secretion of many biotechnologically relevant enzymes that are naturally produced by it or related organisms. However, the use of B. subtilis as a host for production of heterologous secretory proteins can be complicated by problems related to inefficient translocation of the foreign proteins across the plasma membrane or to inefficient release of the exported proteins from the cell surface into the surrounding medium. Therefore, there is a clear need for tools that allow more efficient membrane targeting, translocation, and release during the production of these proteins. In the present study, we investigated the contributions of the pre (pre(lip)) and pro (pro(lip)) sequences of a Staphylococcus hyicus lipase to secretion of a heterologous protein, the alkaline phosphatase PhoA of Escherichia coli, by B. subtilis. The results indicate that the presence of the pro(lip)-peptide, in combination with the lipase signal peptide (pre(lip)), contributes significantly to the efficient secretion of PhoA by B. subtilis and that pre(lip) directs PhoA secretion more efficiently than the authentic signal peptide of PhoA. Genome-wide transcriptional analyses of the host cell responses indicate that, under the conditions tested, no known secretion or membrane-cell wall stress responses were provoked by the production of PhoA with any of the pre- and pro-region sequences used. Our data underscore the view that the pre-pro signals of the S. hyicus lipase are very useful tools for secretion of heterologous proteins in B. subtilis.
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36
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Adrio JL, Demain AL. Recombinant organisms for production of industrial products. Bioeng Bugs 2009; 1:116-31. [PMID: 21326937 DOI: 10.4161/bbug.1.2.10484] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 10/30/2009] [Accepted: 11/02/2009] [Indexed: 11/19/2022] Open
Abstract
A revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of DNA and the development of recombinant DNA technology. Traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. Novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding techniques and their modifications are contributing greatly to the development of improved industrial processes. In addition, functional genomics, proteomics and metabolomics are being exploited for the discovery of novel valuable small molecules for medicine as well as enzymes for catalysis. The sequencing of industrial microbal genomes is being carried out which bodes well for future process improvement and discovery of new industrial products.
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Affiliation(s)
- Jose-Luis Adrio
- NeuronBioPharma, S.A., Parque Tecnologico de Ciencias de la Salud, Edificio BIC, Armilla, Granada, Spain
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37
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Liu Y, Shen W, Shi GY, Wang ZX. Role of the calcium-binding residues Asp231, Asp233, and Asp438 in alpha-amylase of Bacillus amyloliquefaciens as revealed by mutational analysis. Curr Microbiol 2009; 60:162-6. [PMID: 19841977 DOI: 10.1007/s00284-009-9517-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 09/24/2009] [Indexed: 11/26/2022]
Abstract
Role of the calcium-binding residues Asp231, Asp233, and Asp438 of Bacillus amyloliquefaciens alpha-amylase (BAA) on the enzyme properties was investigated by site-directed mutagenesis. The calcium-binding residues Asp231, Asp233, and Asp438 were replaced with Asn, Asn, and Gly to produce the mutants D231N, D233N, and D438G, respectively. The mutant amylases were purified to homogeneity and the purified enzymes was estimated to be approximately 58 kDa. The specific activity for the mutant enzyme D233N was decreased by 84.8%, while D231N and D438G showed a decrease of 6.3% and 3.5% to that of the wild-type enzyme, respectively. No significant changes in the K (m) value, thermo-stability, optimum temperature, and optimum pH were observed in the mutations of D231N and D438G, while substitution of Asp233 with Asn resulted in a dramatic reduction in the value of catalytic efficiency (K (cat)/K (m)) and thermo-stability at 60 degrees C. The ranges of optimum temperature and optimum pH for D233N were also reduced to about 10 degrees C and 3-4 units, respectively.
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Affiliation(s)
- Yang Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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38
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Kouwen TRHM, Antelmann H, van der Ploeg R, Denham EL, Hecker M, van Dijl JM. MscL of Bacillus subtilis prevents selective release of cytoplasmic proteins in a hypotonic environment. Proteomics 2009; 9:1033-43. [DOI: 10.1002/pmic.200800483] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Modulation of thiol-disulfide oxidoreductases for increased production of disulfide-bond-containing proteins in Bacillus subtilis. Appl Environ Microbiol 2008; 74:7536-45. [PMID: 18952880 DOI: 10.1128/aem.00894-08] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Disulfide bonds are important for the correct folding, structural integrity, and activity of many biotechnologically relevant proteins. For synthesis and subsequent secretion of these proteins in bacteria, such as the well-known "cell factory" Bacillus subtilis, it is often the correct formation of disulfide bonds that is the greatest bottleneck. Degradation of inefficiently or incorrectly oxidized proteins and the requirement for costly and time-consuming reduction and oxidation steps in the downstream processing of the proteins still are major limitations for full exploitation of B. subtilis for biopharmaceutical production. Therefore, the present study was aimed at developing a novel in vivo strategy for improved production of secreted disulfide-bond-containing proteins. Three approaches were tested: depletion of the major cytoplasmic reductase TrxA; introduction of the heterologous oxidase DsbA from Staphylococcus carnosus; and addition of redox-active compounds to the growth medium. As shown using the disulfide-bond-containing molecule Escherichia coli PhoA as a model protein, combined use of these three approaches resulted in secretion of amounts of active PhoA that were approximately 3.5-fold larger than the amounts secreted by the parental strain B. subtilis 168. Our findings indicate that Bacillus strains with improved oxidizing properties can be engineered for biotechnological production of heterologous high-value proteins containing disulfide bonds.
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40
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Workman WE, McLinden JH, Dean DH, Copeland JC. Genetic Engineering Applications to Biotechnology in the GenusBacillus. Crit Rev Biotechnol 2008. [DOI: 10.3109/07388558509150784] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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41
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Kodama T, Endo K, Sawada K, Ara K, Ozaki K, Kakeshita H, Yamane K, Sekiguchi J. Bacillus subtilis AprX involved in degradation of a heterologous protein during the late stationary growth phase. J Biosci Bioeng 2007; 104:135-43. [PMID: 17884659 DOI: 10.1263/jbb.104.135] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Accepted: 05/21/2007] [Indexed: 11/17/2022]
Abstract
In Bacillus subtilis, extracellular protease-deficient mutants have been used in attempts to increase the productivity of heterologous proteins. We detected protease activity of AprX using protease zymography in the culture medium at the late stationary growth phase. An alpha-amylase-A522-PreS2 hybrid protein, in which the PreS2 antigen of human hepatitis B virus (HBV) is fused with the N-terminal 522-amino-acid polypeptide of B. subtilis alpha-amylase, has been produced in multiple-protease-deficient mutants. The B. subtilis KA8AX strain, which is deficient in eight extracellular proteases and AprX, did not show the proteolysis of alpha-amylase-A522-PreS2 in the late stationary growth phase. Moreover, the production of alpha-amylase-A522-PreS2 was about 80 mg/l, which was eight times higher than that by the KA8AX strain previously reported. In addition, we showed the degradation of the heterologous protein by AprX that leaked to the culture medium (probably caused by cell lysis) during the late stationary growth phase.
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Affiliation(s)
- Takeko Kodama
- Biological Science Laboratories, Kao Corporation, 2606 Akabane, Ichikai, Haga, Tochigi 321-3497, Japan
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42
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Nguyen HD, Phan TTP, Schumann W. Expression vectors for the rapid purification of recombinant proteins in Bacillus subtilis. Curr Microbiol 2007; 55:89-93. [PMID: 17624574 DOI: 10.1007/s00284-006-0419-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2006] [Accepted: 10/20/2006] [Indexed: 10/23/2022]
Abstract
We describe the construction of six novel plasmid-based IPTG-inducible expression vectors for Bacillus subtilis and related species. While one vector allows intracellular production of recombinant proteins, the second provides a strong secretion signal. The third vector allows addition of the c-Myc epitope tag, and the remaining three vectors provide the purification tags His and Strep. The versatility of all six vectors was demonstrated by the insertion of several reporter genes and by their regulated overexpression. Recombinant proteins with a His- or Strep-tag could be purified to near homogeneity in a single step.
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Affiliation(s)
- Hoang Duc Nguyen
- Institute of Genetics, University of Bayreuth, D-95440, Bayreuth, Germany
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43
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Lulko AT, Veening JW, Buist G, Smits WK, Blom EJ, Beekman AC, Bron S, Kuipers OP. Production and secretion stress caused by overexpression of heterologous alpha-amylase leads to inhibition of sporulation and a prolonged motile phase in Bacillus subtilis. Appl Environ Microbiol 2007; 73:5354-62. [PMID: 17586671 PMCID: PMC1950988 DOI: 10.1128/aem.00472-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptome analysis was used to investigate the global stress response of the gram-positive bacterium Bacillus subtilis caused by overproduction of the well-secreted AmyQ alpha-amylase from Bacillus amyloliquefaciens. Analyses of the control and overproducing strains were carried out at the end of exponential growth and in stationary phase, when protein secretion from B. subtilis is optimal. Among the genes that showed increased expression were htrA and htrB, which are part of the CssRS regulon, which responds to high-level protein secretion and heat stress. The analysis of the transcriptome profiles of a cssS mutant compared to the wild type, under identical secretion stress conditions, revealed several genes with altered transcription in a CssRS-dependent manner, for example, citM, ylxF, yloA, ykoJ, and several genes of the flgB operon. However, high-affinity CssR binding was observed only for htrA, htrB, and, possibly, citM. In addition, the DNA macroarray approach revealed that several genes of the sporulation pathway are downregulated by AmyQ overexpression and that a group of motility-specific (sigmaD-dependent) transcripts were clearly upregulated. Subsequent flow-cytometric analyses demonstrate that, upon overproduction of AmyQ as well as of a nonsecretable variant of the alpha-amylase, the process of sporulation is severely inhibited. Similar experiments were performed to investigate the expression levels of the hag promoter, a well-established reporter for sigmaD-dependent gene expression. This approach confirmed the observations based on our DNA macroarray analyses and led us to conclude that expression levels of several genes involved in motility are maintained at high levels under all conditions of alpha-amylase overproduction.
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Affiliation(s)
- Andrzej T Lulko
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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44
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Waldeck J, Meyer-Rammes H, Wieland S, Feesche J, Maurer KH, Meinhardt F. Targeted deletion of genes encoding extracellular enzymes in Bacillus licheniformis and the impact on the secretion capability. J Biotechnol 2007; 130:124-32. [PMID: 17481763 DOI: 10.1016/j.jbiotec.2007.03.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 02/13/2007] [Accepted: 03/09/2007] [Indexed: 10/23/2022]
Abstract
The general secretory pathway is routinely concerned with a multitude of extracellular enzymes. By eliminating obstructive competitors the export machinery may transport larger quantities of remaining proteins under circumstances in which the secretion machinery is fully loaded. Hence, in this study, genes encoding efficiently expressed but dispensable exoenzymes were knocked out in Bacillus licheniformis MD1. Single, double, and triple mutants with deletions of celA, chiA, and amyB, respectively, were generated via in vivo recombination by making use of a vector with a temperature sensitive origin of replication. Overexpression of a heterologous amylase gene on a multi-copy plasmid, a common scenario in biotechnological processes, resulted in an articulate reduction of chromosomally encoded extracellular enzyme activities indicating that the secretion machinery works to capacity in such transformants. Deletion mutants with the expression plasmid displayed enhanced amylase activities compared to the strain with the wild type genetic background. In addition, the chromosomally encoded protease activity was clearly higher in transformants with deletions.
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Affiliation(s)
- Jens Waldeck
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, Corrensstrasse 3, 48149 Münster, Germany
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45
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AIBA SHUICHI, KOIZUMI JUNICHI, RU JIASHI. ENHANCED PRODUCTION OF α-AMYLASE AND PLASMID STABILITY IN BATCH AND/OR CONTINUOUS CULTURES OF BACILLUS STEAROTHERMOPHILUS (pAT9). CHEM ENG COMMUN 2007. [DOI: 10.1080/00986448608911386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- SHUICHI AIBA
- a Department of Fermentation Technology, Faculty of Engineering , Osaka University , Yamada-Oka, Suita-shi, Osaka, 565, Japan
| | - JUN-ICHI KOIZUMI
- a Department of Fermentation Technology, Faculty of Engineering , Osaka University , Yamada-Oka, Suita-shi, Osaka, 565, Japan
| | - JIA SHI RU
- a Department of Fermentation Technology, Faculty of Engineering , Osaka University , Yamada-Oka, Suita-shi, Osaka, 565, Japan
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46
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Thuy Le AT, Schumann W. A novel cold-inducible expression system for Bacillus subtilis. Protein Expr Purif 2007; 53:264-9. [PMID: 17307364 DOI: 10.1016/j.pep.2006.12.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Revised: 12/19/2006] [Accepted: 12/22/2006] [Indexed: 11/21/2022]
Abstract
Production of recombinant proteins at low temperatures is one strategy to prevent formation of protein aggregates and the use of an expensive inducer such as IPTG. We report on the construction of two expression vectors both containing the cold-inducible des promoter of Bacillus subtilis, where one allows intra- and the other extracellular synthesis of recombinant proteins. Production of recombinant proteins started within the first 30min after temperature downshock to 25 degrees C and continued for about 5h.
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Affiliation(s)
- Ai Thi Thuy Le
- Institute of Genetics, Universität Bayreuth, D-95440 Bayreuth, Germany
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47
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Structural Genomics. CELL ENGINEERING 2007. [PMCID: PMC7122701 DOI: 10.1007/1-4020-5252-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Drug discovery based on structural knowledge has proven useful as several structure-based medicines are already on the market. Structural genomics aims at studying a large number of gene products including whole genomes, topologically similar proteins, protein families and protein subtypes in parallel. Particularly, therapeutically relevant targets have been selected for structural genomics initiatives. In this context, integral membrane proteins, which represent 60–70% of the current drug targets, have been of major interest. Paradoxically, membrane proteins present the last frontier to conquer in structural biology as some 100 high resolution structures among the 30,000 entries in public structural databases are available. The modest success rate on membrane proteins relates to the difficulties in their expression, purification and crystallography. To facilitate technology development large networks providing expertise in molecular biology, protein biochemistry and structural biology have been established. The privately funded MePNet program has studied 100 G protein-coupled receptors, which resulted in high level expression of a large number of receptors at structural biology compatible levels. Currently, selected GPCRs have been purified and subjected to crystallization attempts
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48
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Lindholm A, Ellmén U, Tolonen-Martikainen M, Palva A. Heterologous protein secretion in Lactococcus lactis is enhanced by the Bacillus subtilis chaperone-like protein PrsA. Appl Microbiol Biotechnol 2006; 73:904-14. [PMID: 16944130 DOI: 10.1007/s00253-006-0551-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Revised: 06/18/2006] [Accepted: 06/19/2006] [Indexed: 10/24/2022]
Abstract
The Bacillus subtilis lipoprotein PrsA enhances the yield of several homologous and heterologous exported proteins in B. subtilis by being involved in the posttranslocational stage of the secretion process. In this work, we have studied the effect of B. subtilis PrsA on the secretion of Bacillus amyloliquefaciens alpha-amylase (AmyQ), a target protein for PrsA, and Bacillus licheniformis penicillinase (PenP) a nontarget protein for PrsA, in Lactococcus lactis. Two compatible plasmids were constructed and introduced into L. lactis strain NZ9000: one high copy plasmid, expressing the AmyQ gene (amyQ) or the PenP gene (penP), and one low copy plasmid, expressing the PrsA encoding gene (prsA). When amyQ and prsA were simultaneously expressed under the nisin-inducible promoter P( nisA ), Western blotting experiments revealed a 15- to 20-fold increase in the total yield of AmyQ and a sixfold increase in secreted AmyQ activity, compared to a control strain lacking prsA. When expressed under the same induction conditions, PrsA had no effect on the secretion or total yield of PenP. These results show that the secretion yield of some heterologous proteins can be significantly increased in L. lactis when coproduced with the B. subtilis PrsA protein.
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Affiliation(s)
- Agneta Lindholm
- Division of Microbiology and Epidemiology, Department of Basic Veterinary Sciences, University of Helsinki, Helsinki 00014, Finland
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49
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Zanen G, Antelmann H, Meima R, Jongbloed JDH, Kolkman M, Hecker M, van Dijl JM, Quax WJ. Proteomic dissection of potential signal recognition particle dependence in protein secretion by Bacillus subtilis. Proteomics 2006; 6:3636-48. [PMID: 16705751 DOI: 10.1002/pmic.200500560] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The bacterial signal recognition particle (SRP)-dependent pathway is believed to be a major targeting route for membrane proteins, as well as for subsets of secretory proteins. The present studies were aimed at an assessment of the role of two key components of SRP, namely Ffh and FtsY, in protein secretion by the Gram-positive bacterium Bacillus subtilis. Our results show that both components are important for the extracellular accumulation of proteins containing known signal peptides. Remarkably, extracellular accumulation of individual proteins was affected to different extents by depletion of Ffh or FtsY, at least under the conditions tested. Moreover, the observed Ffh or FtsY dependence of certain secretory proteins did not seem to correlate with signal peptide length or hydrophobicity. Although it is presently difficult to distinguish between direct and indirect effects, these findings suggest that other, yet unidentified, determinants in secretory proteins are also important for their SRP dependence. High-level production of homologous and heterologous secretory proteins was shown to result in elevated cellular Ffh and FtsY levels. This phenomenon is, most likely, due to post-transcriptional regulation. In conclusion, the present proteomic dissection of SRP-dependent extracellular protein accumulation provides exciting leads to identify novel determinants for interactions between secretory proteins and SRP.
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Affiliation(s)
- Geeske Zanen
- Department of Pharmaceutical Biology, University of Groningen, The Netherlands
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50
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Terpe K. Overview of bacterial expression systems for heterologous protein production: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol 2006; 72:211-22. [PMID: 16791589 DOI: 10.1007/s00253-006-0465-8] [Citation(s) in RCA: 630] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 04/18/2006] [Accepted: 04/19/2006] [Indexed: 11/28/2022]
Abstract
During the proteomics period, the growth in the use of recombinant proteins has increased greatly in the recent years. Bacterial systems remain most attractive due to low cost, high productivity, and rapid use. However, the rational choice of the adequate promoter system and host for a specific protein of interest remains difficult. This review gives an overview of the most commonly used systems: As hosts, Bacillus brevis, Bacillus megaterium, Bacillus subtilis, Caulobacter crescentus, other strains, and, most importantly, Escherichia coli BL21 and E. coli K12 and their derivatives are presented. On the promoter side, the main features of the l-arabinose inducible araBAD promoter (PBAD), the lac promoter, the l-rhamnose inducible rhaP BAD promoter, the T7 RNA polymerase promoter, the trc and tac promoter, the lambda phage promoter p L , and the anhydrotetracycline-inducible tetA promoter/operator are summarized.
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Affiliation(s)
- Kay Terpe
- IBA GmbH, 37079, Göttingen, Germany.
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